Pinder system

from pathlib import Path

from pinder.core import PinderSystem, get_index

Example usage of Pinder index API shown below. For more detailed usage examples, check the pinder-indexnotebook.

index = get_index()
hetero_test_apo = index.query(
    '(uniprot_L != uniprot_R) and split == "test" and (apo_R and apo_L)'
)
hetero_test_apo.reset_index(drop=True, inplace=True)
hetero_test_apo

	split	id	pdb_id	cluster_id	cluster_id_R	cluster_id_L	pinder_s	pinder_xl	pinder_af2	uniprot_R	...	apo_L	apo_R_quality	apo_L_quality	chain1_neff	chain2_neff	chain_R	chain_L	contains_antibody	contains_antigen	contains_enzyme
0	test	3k1i__D1_O25709--3k1i__A1_O25448	3k1i	cluster_26031_5179	cluster_26031	cluster_5179	True	True	False	O25709	...	True	high	high	12.351562	514.000000	D1	A1	False	False	False
1	test	6qta__A1_G0SHE6--6qta__B1_G0SC29	6qta	cluster_11327_11328	cluster_11327	cluster_11328	False	True	False	G0SHE6	...	True	high	high	115.750000	689.500000	A1	B1	False	False	False
2	test	3vf0__B1_Q8IY67--3vf0__A2_P18206	3vf0	cluster_5612_993	cluster_993	cluster_5612	True	True	False	Q8IY67	...	True	high	high	251.125000	35.531250	B1	A2	False	False	False
3	test	4aye__D1_Q9JXV4--4aye__A1_P08603	4aye	cluster_3949_4866	cluster_3949	cluster_4866	True	True	False	Q9JXV4	...	True	high	high	14.546875	310.000000	D1	A1	False	False	False
4	test	2w8b__A1_P0A855--2w8b__H1_P0A912	2w8b	cluster_15535_1924	cluster_15535	cluster_1924	True	True	False	P0A855	...	True	high	high	308.250000	1150.000000	A1	H1	False	False	False
5	test	5y4r__A1_O87131--5y4r__B1_Q9HVI1	5y4r	cluster_8825_8826	cluster_8825	cluster_8826	True	True	False	O87131	...	True	high	high	610.000000	144.875000	A1	B1	False	False	True
6	test	3egv__A1_Q84BQ9--3egv__B1_Q5SLP6	3egv	cluster_33015_371	cluster_33015	cluster_371	True	True	False	Q84BQ9	...	True	high	high	806.500000	637.000000	A1	B1	False	False	True
7	test	6wjc__A1_P11229--6wjc__B1_Q8QGR0	6wjc	cluster_1057_1356	cluster_1057	cluster_1356	True	True	False	P11229	...	True	high	high	462.750000	518.500000	A1	B1	False	False	True
8	test	6tx3__B1_Q9NWY4--6tx3__A1_Q9UGN5	6tx3	cluster_11866_335	cluster_11866	cluster_335	True	True	False	Q9NWY4	...	True	high	high	59.468750	213.000000	B1	A1	False	False	True
9	test	2grx__A1_P06971--2grx__C1_P02929	2grx	cluster_12107_8897	cluster_12107	cluster_8897	True	True	False	P06971	...	True	high	high	288.000000	562.500000	A1	C1	False	False	False
10	test	3kbu__A1_P11277--3kbu__D1_P16157	3kbu	cluster_16732_8658	cluster_8658	cluster_16732	True	True	False	P11277	...	True	high	high	229.625000	210.625000	A1	D1	False	False	False
11	test	2j0t__A1_P03956--2j0t__D1_P01033	2j0t	cluster_939_940	cluster_939	cluster_940	True	True	False	P03956	...	True	high	high	612.500000	68.312500	A1	D1	False	False	True
12	test	8a60__A1_P06971--8a60__B1_Q38162	8a60	cluster_12107_26846	cluster_12107	cluster_26846	False	True	True	P06971	...	True	high	high	288.000000	2.734375	A1	B1	False	False	False
13	test	4je4__A1_Q06124--4je4__B1_P02751	4je4	cluster_1465_1605	cluster_1465	cluster_1605	True	True	False	Q06124	...	True	high	high	611.000000	75.062500	A1	B1	False	False	False
14	test	4uae__A1_O00629--4uae__B1_P31345	4uae	cluster_10331_1373	cluster_1373	cluster_10331	False	True	False	O00629	...	True	high	high	240.750000	3.058594	A1	B1	False	False	False
15	test	3k9m__A1_P07858--3k9m__B1_P01040	3k9m	cluster_4628_6704	cluster_6704	cluster_4628	True	True	False	P07858	...	True	high	high	770.000000	429.750000	A1	B1	False	False	True
16	test	2wo2__A1_P54764--2wo2__B1_P52799	2wo2	cluster_130_8064	cluster_130	cluster_8064	True	True	False	P54764	...	True	high	high	567.500000	104.562500	A1	B1	False	False	True
17	test	5dob__A1_P16794--5dob__B1_P16791	5dob	cluster_12247_23692	cluster_12247	cluster_23692	False	True	False	P16794	...	True	high	high	3.312500	3.855469	A1	B1	False	False	False
18	test	8i2e__A1_O34841--8i2e__B1_P54421	8i2e	cluster_11087_12465	cluster_12465	cluster_11087	True	True	True	O34841	...	True	high	high	9.031250	865.000000	A1	B1	False	False	True
19	test	1zlh__A1_P00730--1zlh__B1_Q5EPH2	1zlh	cluster_2416_8594	cluster_2416	cluster_8594	True	True	False	P00730	...	True	high	high	541.000000	637.000000	A1	B1	False	False	True
20	test	6yev__C1_P0A744--6yev__A1_P0AA25	6yev	cluster_4231_621	cluster_4231	cluster_621	True	True	False	P0A744	...	True	high	high	1099.000000	1440.000000	C1	A1	False	False	True
21	test	1dtd__A1_P48052--1dtd__B1_P81511	1dtd	cluster_2416_9476	cluster_2416	cluster_9476	True	True	False	P48052	...	True	high	high	581.000000	8.781250	A1	B1	False	False	True
22	test	7fn1__B1_P32357--7fn1__A1_P33334	7fn1	cluster_635_7263	cluster_7263	cluster_635	True	True	False	P32357	...	True	high	high	8.070312	69.062500	B1	A1	False	False	False
23	test	1yu6__A1_P00780--1yu6__C1_P68390	1yu6	cluster_1952_5091	cluster_1952	cluster_5091	True	True	False	P00780	...	True	high	high	1000.000000	704.000000	A1	C1	False	False	True
24	test	6s8v__B1_P08195--6s8v__A1_P80188	6s8v	cluster_19347_5331	cluster_19347	cluster_5331	True	True	False	P08195	...	True	high	high	511.000000	34.812500	B1	A1	False	False	False
25	test	5ja2__A1_P11454--5ja2__B1_Q9I169	5ja2	cluster_4489_7234	cluster_7234	cluster_4489	True	True	False	P11454	...	True	high	high	641.500000	545.500000	A1	B1	False	False	True
26	test	6f3z__A1_P0ADC3--6f3z__B1_P61316	6f3z	cluster_12985_22189	cluster_22189	cluster_12985	True	True	False	P0ADC3	...	True	high	high	402.500000	368.000000	A1	B1	False	False	False
27	test	8gt0__A1_Q8I6U4--8gt0__B1_P01040	8gt0	cluster_2085_4628	cluster_2085	cluster_4628	True	True	False	Q8I6U4	...	True	high	high	651.000000	429.750000	A1	B1	False	False	True
28	test	2gkv__A1_P00777--2gkv__B1_P68390	2gkv	cluster_5091_5268	cluster_5268	cluster_5091	True	True	False	P00777	...	True	high	high	409.000000	704.000000	A1	B1	False	False	True
29	test	6m4v__A1_P0AEX9--6m4v__B1_P62942	6m4v	cluster_1772_409	cluster_409	cluster_1772	True	True	False	P0AEX9	...	True	high	high	171.250000	1408.000000	A1	B1	False	False	True
30	test	4us1__B1_Q07889--4us1__A1_P01112	4us1	cluster_10806_437	cluster_10806	cluster_437	True	True	False	Q07889	...	True	high	high	183.375000	946.500000	B1	A1	False	False	False
31	test	1tec__A1_P04072--1tec__B1_P01051	1tec	cluster_1952_387	cluster_1952	cluster_387	True	True	False	P04072	...	True	high	high	1017.500000	133.750000	A1	B1	False	False	True
32	test	1zhh__A1_P54300--1zhh__B1_P54302	1zhh	cluster_3962_8641	cluster_3962	cluster_8641	True	True	False	P54300	...	True	high	high	23.531250	524.500000	A1	B1	False	False	False
33	test	5n47__B1_P02751--5n47__A1_P80188	5n47	cluster_1605_5331	cluster_1605	cluster_5331	True	True	False	P02751	...	True	high	high	75.062500	34.812500	B1	A1	False	False	False
34	test	7b80__A1_G3I8R9--7b80__B1_Q9BVA6	7b80	cluster_1039_643	cluster_643	cluster_1039	True	True	False	G3I8R9	...	True	high	high	1069.000000	526.500000	A1	B1	False	False	True

35 rows × 34 columns

pinder_id = list(hetero_test_apo.id)[2]
pinder_id

'3vf0__B1_Q8IY67--3vf0__A2_P18206'

PinderSystem API - base class representing Structure’s in a pinder entry

# Simplest interface - get a single pinder system
ps = PinderSystem(pinder_id)
ps

2024-09-13 20:42:03,790 | pinder.core.utils.cloud:375 | INFO : Gsutil process_many=download_to_filename, threads=4, items=15

2024-09-13 20:42:04,283 | pinder.core.utils.cloud.process_many:23 | INFO : runtime succeeded:      0.49s

PinderSystem(
entry = IndexEntry(
    (
        'split',
        'test',
    ),
    (
        'id',
        '3vf0__B1_Q8IY67--3vf0__A2_P18206',
    ),
    (
        'pdb_id',
        '3vf0',
    ),
    (
        'cluster_id',
        'cluster_5612_993',
    ),
    (
        'cluster_id_R',
        'cluster_993',
    ),
    (
        'cluster_id_L',
        'cluster_5612',
    ),
    (
        'pinder_s',
        True,
    ),
    (
        'pinder_xl',
        True,
    ),
    (
        'pinder_af2',
        False,
    ),
    (
        'uniprot_R',
        'Q8IY67',
    ),
    (
        'uniprot_L',
        'P18206',
    ),
    (
        'holo_R_pdb',
        '3vf0__B1_Q8IY67-R.pdb',
    ),
    (
        'holo_L_pdb',
        '3vf0__A2_P18206-L.pdb',
    ),
    (
        'predicted_R_pdb',
        'af__Q8IY67.pdb',
    ),
    (
        'predicted_L_pdb',
        'af__P18206.pdb',
    ),
    (
        'apo_R_pdb',
        '3smz__A1_Q8IY67.pdb',
    ),
    (
        'apo_L_pdb',
        '5l0h__A1_P18206.pdb',
    ),
    (
        'apo_R_pdbs',
        '3smz__A1_Q8IY67.pdb',
    ),
    (
        'apo_L_pdbs',
        '5l0h__A1_P18206.pdb;5l0f__A1_P18206.pdb;5l0i__A1_P18206.pdb',
    ),
    (
        'holo_R',
        True,
    ),
    (
        'holo_L',
        True,
    ),
    (
        'predicted_R',
        True,
    ),
    (
        'predicted_L',
        True,
    ),
    (
        'apo_R',
        True,
    ),
    (
        'apo_L',
        True,
    ),
    (
        'apo_R_quality',
        'high',
    ),
    (
        'apo_L_quality',
        'high',
    ),
    (
        'chain1_neff',
        251.125,
    ),
    (
        'chain2_neff',
        35.53125,
    ),
    (
        'chain_R',
        'B1',
    ),
    (
        'chain_L',
        'A2',
    ),
    (
        'contains_antibody',
        False,
    ),
    (
        'contains_antigen',
        False,
    ),
    (
        'contains_enzyme',
        False,
    ),
)
native=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/3vf0__B1_Q8IY67--3vf0__A2_P18206.pdb,
    uniprot_map=None,
    pinder_id='3vf0__B1_Q8IY67--3vf0__A2_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (3584,),
    pdb_engine='fastpdb',
)
holo_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/test_set_pdbs/3vf0__B1_Q8IY67-R.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/3vf0__B1_Q8IY67-R.parquet,
    pinder_id='3vf0__B1_Q8IY67-R',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (2204,),
    pdb_engine='fastpdb',
)
holo_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/test_set_pdbs/3vf0__A2_P18206-L.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/3vf0__A2_P18206-L.parquet,
    pinder_id='3vf0__A2_P18206-L',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1380,),
    pdb_engine='fastpdb',
)
apo_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/3smz__A1_Q8IY67.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/3smz__A1_Q8IY67.parquet,
    pinder_id='3smz__A1_Q8IY67',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (2183,),
    pdb_engine='fastpdb',
)
apo_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/5l0h__A1_P18206.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/5l0h__A1_P18206.parquet,
    pinder_id='5l0h__A1_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1341,),
    pdb_engine='fastpdb',
)
pred_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/af__Q8IY67.pdb,
    uniprot_map=None,
    pinder_id='af__Q8IY67',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (4495,),
    pdb_engine='fastpdb',
)
pred_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/af__P18206.pdb,
    uniprot_map=None,
    pinder_id='af__P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (8664,),
    pdb_engine='fastpdb',
)
)

holo_L, holo_R = ps.holo_ligand, ps.holo_receptor
pred_L, pred_R = ps.pred_ligand, ps.pred_receptor
apo_L, apo_R = ps.apo_ligand, ps.apo_receptor

holo_L

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/test_set_pdbs/3vf0__A2_P18206-L.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/3vf0__A2_P18206-L.parquet,
    pinder_id='3vf0__A2_P18206-L',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1380,),
    pdb_engine='fastpdb',
)

Classify system difficulty based on degree of conformational shift in unbound and bound

ps.unbound_difficulty("apo")

{'Fnat': 0.5421686746987951,
 'Fnonnat': 0.3076923076923077,
 'common_contacts': 45,
 'differing_contacts': 20,
 'bound_contacts': 83,
 'unbound_contacts': 65,
 'fnonnat_R': 0.2857142857142857,
 'fnonnat_L': 0.0,
 'fnat_R': 0.5882352941176471,
 'fnat_L': 0.7692307692307693,
 'difficulty': 'Rigid-body',
 'I-RMSD': 1.125529,
 'matched_interface_chains': 2,
 'holo_receptor_interface_res': 34,
 'holo_ligand_interface_res': 26,
 'apo_receptor_interface_res': 28,
 'apo_ligand_interface_res': 20,
 'L-RMSD': 0.94191533,
 'R-RMSD': 1.4988925,
 'unbound_id': '3smz__A1_Q8IY67--5l0h__A1_P18206',
 'unbound_body': 'receptor_ligand',
 'monomer_name': 'apo'}

ps.unbound_difficulty("predicted")

{'Fnat': 0.5662650602409639,
 'Fnonnat': 0.9225700164744646,
 'common_contacts': 47,
 'differing_contacts': 560,
 'bound_contacts': 83,
 'unbound_contacts': 607,
 'fnonnat_R': 0.8435374149659864,
 'fnonnat_L': 0.8670520231213873,
 'fnat_R': 0.6764705882352942,
 'fnat_L': 0.8846153846153846,
 'difficulty': 'Difficult',
 'I-RMSD': 3.4248848,
 'matched_interface_chains': 2,
 'holo_receptor_interface_res': 34,
 'holo_ligand_interface_res': 26,
 'apo_receptor_interface_res': 147,
 'apo_ligand_interface_res': 173,
 'L-RMSD': 2.1201644,
 'R-RMSD': 0.62853533,
 'unbound_id': 'af__Q8IY67--af__P18206',
 'unbound_body': 'receptor_ligand',
 'monomer_name': 'predicted'}

Illustrating utilities available in Structure instances

holo_L.filter("atom_name", mask=["CA"])

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/test_set_pdbs/3vf0__A2_P18206-L.pdb,
    uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (283, 14),
    pinder_id='3vf0__A2_P18206-L',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (178,),
    pdb_engine='fastpdb',
)

apo_L.filter("atom_name", mask=["CA"])

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/5l0h__A1_P18206.pdb,
    uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (176, 14),
    pinder_id='5l0h__A1_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (173,),
    pdb_engine='fastpdb',
)

Can also filter “in place” rather than returning a copy (a la pandas)

apo_L.filter("atom_name", mask=["CA"], copy=False)

(
    ps.apo_ligand.filter("atom_name", mask=["CA"]),
    ps.holo_ligand.filter("atom_name", mask=["CA"])
)

(Structure(
     filepath=/home/runner/.local/share/pinder/2024-02/pdbs/5l0h__A1_P18206.pdb,
     uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (176, 14),
     pinder_id='5l0h__A1_P18206',
     atom_array=<class 'biotite.structure.AtomArray'> with shape (173,),
     pdb_engine='fastpdb',
 ),
 Structure(
     filepath=/home/runner/.local/share/pinder/2024-02/test_set_pdbs/3vf0__A2_P18206-L.pdb,
     uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (283, 14),
     pinder_id='3vf0__A2_P18206-L',
     atom_array=<class 'biotite.structure.AtomArray'> with shape (178,),
     pdb_engine='fastpdb',
 ))

Create masked unbound complex aligned to bound for apo

apo_complex = ps.create_apo_complex()
apo_complex

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/3smz__A1_Q8IY67--5l0h__A1_P18206.pdb,
    uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (460, 14),
    pinder_id='3smz__A1_Q8IY67--5l0h__A1_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (2355,),
    pdb_engine='fastpdb',
)

apo_complex.dataframe

	chain_id	res_name	res_code	res_id	atom_name	b_factor	ins_code	hetero	element	x	y	z
0	R	HIS	H	1	N	0.0		False	N	69.377380	105.086411	-51.232784
1	R	HIS	H	1	CA	0.0		False	C	69.471100	103.738152	-50.680832
2	R	HIS	H	1	C	0.0		False	C	70.264641	103.716263	-49.368168
3	R	HIS	H	1	O	0.0		False	O	70.223633	102.714134	-48.653946
4	R	HIS	H	1	CB	0.0		False	C	70.093376	102.773239	-51.701912
...	...	...	...	...	...	...	...	...	...	...	...	...
2350	L	ARG	R	170	CA	0.0		False	C	45.438423	86.089317	-54.533417
2351	L	LYS	K	171	CA	0.0		False	C	44.941048	83.492149	-57.280712
2352	L	THR	T	172	CA	0.0		False	C	46.387222	85.555809	-60.138439
2353	L	PRO	P	173	CA	0.0		False	C	49.873409	84.154137	-59.526482
2354	L	TRP	W	174	CA	0.0		False	C	50.158199	80.451759	-60.405190

2355 rows × 12 columns

What’s going on under the hood

ps = PinderSystem(pinder_id)
apo_L, apo_R = ps.apo_ligand, ps.apo_receptor

# After getting the "in common" masked structures, they can be superimposed
apo_R, holo_R = apo_R.align_common_sequence(ps.aligned_holo_R)
apo_L, holo_L = apo_L.align_common_sequence(ps.aligned_holo_L)

# Rmsd after superposition (without outlier removal) is stored in `rms`
R_super, rms, _ = apo_R.superimpose(holo_R)
L_super, rms, _ = apo_L.superimpose(holo_L)

L_super

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/5l0h__A1_P18206.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/5l0h__A1_P18206.parquet,
    pinder_id='5l0h__A1_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1327,),
    pdb_engine='fastpdb',
)

# Now we can create the complexes using Structure.__add__ methods
apo_binary = R_super + L_super
holo_binary = holo_R + holo_L

apo_binary

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/3smz__A1_Q8IY67--5l0h__A1_P18206.pdb,
    uniprot_map=<class 'pandas.core.frame.DataFrame'> with shape (460, 14),
    pinder_id='3smz__A1_Q8IY67--5l0h__A1_P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (3510,),
    pdb_engine='fastpdb',
)

# Alternatively, there exist utils for creating the masked apo and predicted complex
pred_complex = ps.create_pred_complex()
pred_complex

Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/af__Q8IY67--af__P18206.pdb,
    uniprot_map=None,
    pinder_id='af__Q8IY67--af__P18206',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (3566,),
    pdb_engine='fastpdb',
)

masked_complex_dir = Path("./").absolute() / "unbound_complexes"
masked_complex_dir.mkdir(exist_ok=True, parents=True)

masked_complex_dir

PosixPath('/home/runner/work/pinder/pinder/docs/unbound_complexes')

# If the output PDB filepath is omitted, the structure will be written to Structure.filepath, which may overwrite
# In this case, it would be a new file composed of the added complex filepaths if we omit
pred_complex.to_pdb(masked_complex_dir / "pred_complex.pdb")
apo_complex.to_pdb(masked_complex_dir / "apo_complex.pdb")

(masked_complex_dir / "pred_complex.pdb").unlink()
(masked_complex_dir / "apo_complex.pdb").unlink()

Structures have resolved_pdb2uniprot and resolved_uniprot2pdb properties

They return dicts of resolved residue numbers mapped from pdb numbering to uniprot numbering, and vice versa

The full mapping is available in Structure.uniprot_mapping To get only the resolved mapping, access the Structure.resolved_mapping attrribute.

apo_L.resolved_pdb2uniprot

{2: 960,
 3: 961,
 4: 962,
 5: 963,
 6: 964,
 7: 965,
 8: 966,
 9: 967,
 10: 968,
 11: 969,
 12: 970,
 13: 971,
 14: 972,
 15: 973,
 16: 974,
 18: 976,
 19: 977,
 20: 978,
 21: 979,
 22: 980,
 23: 981,
 24: 982,
 25: 983,
 26: 984,
 27: 985,
 28: 986,
 29: 987,
 30: 988,
 31: 989,
 32: 990,
 33: 991,
 34: 992,
 35: 993,
 36: 994,
 37: 995,
 38: 996,
 39: 997,
 40: 998,
 41: 999,
 42: 1000,
 43: 1001,
 44: 1002,
 45: 1003,
 46: 1004,
 47: 1005,
 48: 1006,
 49: 1007,
 50: 1008,
 51: 1009,
 52: 1010,
 53: 1011,
 54: 1012,
 55: 1013,
 56: 1014,
 57: 1015,
 58: 1016,
 59: 1017,
 60: 1018,
 61: 1019,
 62: 1020,
 63: 1021,
 64: 1022,
 65: 1023,
 66: 1024,
 67: 1025,
 68: 1026,
 69: 1027,
 70: 1028,
 71: 1029,
 72: 1030,
 73: 1031,
 74: 1032,
 75: 1033,
 76: 1034,
 77: 1035,
 78: 1036,
 79: 1037,
 80: 1038,
 81: 1039,
 82: 1040,
 83: 1041,
 84: 1042,
 85: 1043,
 86: 1044,
 87: 1045,
 88: 1046,
 89: 1047,
 90: 1048,
 91: 1049,
 92: 1050,
 93: 1051,
 94: 1052,
 95: 1053,
 96: 1054,
 97: 1055,
 98: 1056,
 99: 1057,
 100: 1058,
 101: 1059,
 102: 1060,
 103: 1061,
 104: 1062,
 105: 1063,
 106: 1064,
 107: 1065,
 108: 1066,
 109: 1067,
 110: 1068,
 111: 1069,
 112: 1070,
 113: 1071,
 114: 1072,
 115: 1073,
 116: 1074,
 117: 1075,
 118: 1076,
 119: 1077,
 120: 1078,
 121: 1079,
 122: 1080,
 123: 1081,
 124: 1082,
 125: 1083,
 126: 1084,
 127: 1085,
 128: 1086,
 129: 1087,
 130: 1088,
 131: 1089,
 132: 1090,
 133: 1091,
 134: 1092,
 135: 1093,
 136: 1094,
 137: 1095,
 138: 1096,
 139: 1097,
 140: 1098,
 141: 1099,
 142: 1100,
 143: 1101,
 144: 1102,
 145: 1103,
 146: 1104,
 147: 1105,
 148: 1106,
 149: 1107,
 150: 1108,
 151: 1109,
 152: 1110,
 153: 1111,
 154: 1112,
 155: 1113,
 156: 1114,
 157: 1115,
 158: 1116,
 159: 1117,
 160: 1118,
 161: 1119,
 162: 1120,
 163: 1121,
 164: 1122,
 165: 1123,
 166: 1124,
 167: 1125,
 168: 1126,
 169: 1127,
 170: 1128,
 171: 1129,
 172: 1130,
 173: 1131,
 174: 1132}

apo_complex.resolved_mapping

	entry_id	entity_id	asym_id	pdb_strand_id	resi	resi_pdb	resi_auth	resn	one_letter_code_can	resolved	one_letter_code_uniprot	resi_uniprot	uniprot_acc	chain
0	NaN	1	A	A	3	39	39.0	LEU	L	1	L	39	NaN	A1
1	NaN	1	A	A	4	40	40.0	ASP	D	1	D	40	NaN	A1
2	NaN	1	A	A	5	41	41.0	PRO	P	1	P	41	NaN	A1
3	NaN	1	A	A	6	42	42.0	GLU	E	1	E	42	NaN	A1
4	NaN	1	A	A	7	43	43.0	GLU	E	1	E	43	NaN	A1
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
446	NaN	1	A	A	170	1128	1128.0	ARG	R	1	R	1128	NaN	A1
447	NaN	1	A	A	171	1129	1129.0	LYS	K	1	K	1129	NaN	A1
448	NaN	1	A	A	172	1130	1130.0	THR	T	1	T	1130	NaN	A1
449	NaN	1	A	A	173	1131	1131.0	PRO	P	1	P	1131	NaN	A1
450	NaN	1	A	A	174	1132	1132.0	TRP	W	1	W	1132	NaN	A1

451 rows × 14 columns

Case with multiple available apo structures

pinder_id = "1ldt__A1_P00761--1ldt__B1_P80424"

ps_canon = PinderSystem(pinder_id)
ps_canon.entry.apo_R_alt

2024-09-13 20:42:06,606 | pinder.core.utils.cloud:375 | INFO : Gsutil process_many=download_to_filename, threads=4, items=43

2024-09-13 20:42:08,043 | pinder.core.utils.cloud.process_many:23 | INFO : runtime succeeded:      1.44s

['1s6f__A1_P00761.pdb',
 '1s85__A1_P00761.pdb',
 '1s84__A1_P00761.pdb',
 '2a32__A1_P00761.pdb',
 '1s6h__A1_P00761.pdb',
 '1s5s__A1_P00761.pdb',
 '1fni__A1_P00761.pdb',
 '1s81__A1_P00761.pdb',
 '1fmg__A1_P00761.pdb',
 '1qqu__A1_P00761.pdb',
 '2a31__A1_P00761.pdb',
 '1fn6__A1_P00761.pdb',
 '1s83__A1_P00761.pdb']

ps_canon.entry.apo_L_alt

['2kmq__A1_P80424.pdb', '2kmp__A1_P80424.pdb', '2kmr__A1_P80424.pdb']

Specify 2kmr as apo ligand and 1fmg as apo receptor

Note: the default apo_receptor and apo_ligand are determined based on the selected canonical apo monomer.

The canonical monomers were selected based on their sequence overlap and difficulty metrics calculated in pinder.eval.dockq.unbound

ps = PinderSystem(pinder_id, apo_ligand_pdb_code="2kmr", apo_receptor_pdb_code="1fmg")
ps

PinderSystem(
entry = IndexEntry(
    (
        'split',
        'train',
    ),
    (
        'id',
        '1ldt__A1_P00761--1ldt__B1_P80424',
    ),
    (
        'pdb_id',
        '1ldt',
    ),
    (
        'cluster_id',
        'cluster_312_5091',
    ),
    (
        'cluster_id_R',
        'cluster_312',
    ),
    (
        'cluster_id_L',
        'cluster_5091',
    ),
    (
        'pinder_s',
        False,
    ),
    (
        'pinder_xl',
        False,
    ),
    (
        'pinder_af2',
        False,
    ),
    (
        'uniprot_R',
        'P00761',
    ),
    (
        'uniprot_L',
        'P80424',
    ),
    (
        'holo_R_pdb',
        '1ldt__A1_P00761-R.pdb',
    ),
    (
        'holo_L_pdb',
        '1ldt__B1_P80424-L.pdb',
    ),
    (
        'predicted_R_pdb',
        'af__P00761.pdb',
    ),
    (
        'predicted_L_pdb',
        'af__P80424.pdb',
    ),
    (
        'apo_R_pdb',
        '1s82__A1_P00761.pdb',
    ),
    (
        'apo_L_pdb',
        '2kmo__A1_P80424.pdb',
    ),
    (
        'apo_R_pdbs',
        '1s82__A1_P00761.pdb;1s6f__A1_P00761.pdb;1s85__A1_P00761.pdb;1s84__A1_P00761.pdb;2a32__A1_P00761.pdb;1s6h__A1_P00761.pdb;1s5s__A1_P00761.pdb;1fni__A1_P00761.pdb;1s81__A1_P00761.pdb;1fmg__A1_P00761.pdb;1qqu__A1_P00761.pdb;2a31__A1_P00761.pdb;1fn6__A1_P00761.pdb;1s83__A1_P00761.pdb',
    ),
    (
        'apo_L_pdbs',
        '2kmo__A1_P80424.pdb;2kmq__A1_P80424.pdb;2kmp__A1_P80424.pdb;2kmr__A1_P80424.pdb',
    ),
    (
        'holo_R',
        True,
    ),
    (
        'holo_L',
        True,
    ),
    (
        'predicted_R',
        True,
    ),
    (
        'predicted_L',
        True,
    ),
    (
        'apo_R',
        True,
    ),
    (
        'apo_L',
        True,
    ),
    (
        'apo_R_quality',
        'high',
    ),
    (
        'apo_L_quality',
        'high',
    ),
    (
        'chain1_neff',
        997.0,
    ),
    (
        'chain2_neff',
        2220.0,
    ),
    (
        'chain_R',
        'A1',
    ),
    (
        'chain_L',
        'B1',
    ),
    (
        'contains_antibody',
        False,
    ),
    (
        'contains_antigen',
        False,
    ),
    (
        'contains_enzyme',
        True,
    ),
)
native=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/1ldt__A1_P00761--1ldt__B1_P80424.pdb,
    uniprot_map=None,
    pinder_id='1ldt__A1_P00761--1ldt__B1_P80424',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1992,),
    pdb_engine='fastpdb',
)
holo_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/1ldt__A1_P00761-R.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/1ldt__A1_P00761-R.parquet,
    pinder_id='1ldt__A1_P00761-R',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1666,),
    pdb_engine='fastpdb',
)
holo_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/1ldt__B1_P80424-L.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/1ldt__B1_P80424-L.parquet,
    pinder_id='1ldt__B1_P80424-L',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (326,),
    pdb_engine='fastpdb',
)
apo_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/1fmg__A1_P00761.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/1fmg__A1_P00761.parquet,
    pinder_id='1fmg__A1_P00761',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1642,),
    pdb_engine='fastpdb',
)
apo_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/2kmr__A1_P80424.pdb,
    uniprot_map=/home/runner/.local/share/pinder/2024-02/mappings/2kmr__A1_P80424.parquet,
    pinder_id='2kmr__A1_P80424',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (630,),
    pdb_engine='fastpdb',
)
pred_receptor=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/af__P00761.pdb,
    uniprot_map=None,
    pinder_id='af__P00761',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (1708,),
    pdb_engine='fastpdb',
)
pred_ligand=Structure(
    filepath=/home/runner/.local/share/pinder/2024-02/pdbs/af__P80424.pdb,
    uniprot_map=None,
    pinder_id='af__P80424',
    atom_array=<class 'biotite.structure.AtomArray'> with shape (326,),
    pdb_engine='fastpdb',
)
)

Classify system difficulty based on degree of conformational shift in unbound and bound

ps.unbound_difficulty("apo")

{'Fnat': 0.847457627118644,
 'Fnonnat': 0.5,
 'common_contacts': 50,
 'differing_contacts': 50,
 'bound_contacts': 59,
 'unbound_contacts': 100,
 'fnonnat_R': 0.4318181818181818,
 'fnonnat_L': 0.35,
 'fnat_R': 0.8620689655172413,
 'fnat_L': 1.0,
 'difficulty': 'Difficult',
 'I-RMSD': 2.3008883,
 'matched_interface_chains': 2,
 'holo_receptor_interface_res': 29,
 'holo_ligand_interface_res': 13,
 'apo_receptor_interface_res': 44,
 'apo_ligand_interface_res': 20,
 'L-RMSD': 9.371291,
 'R-RMSD': 0.47199312,
 'unbound_id': '1fmg__A1_P00761--2kmr__A1_P80424',
 'unbound_body': 'receptor_ligand',
 'monomer_name': 'apo'}

ps.unbound_difficulty("predicted")

{'Fnat': 0.847457627118644,
 'Fnonnat': 0.05660377358490566,
 'common_contacts': 50,
 'differing_contacts': 3,
 'bound_contacts': 59,
 'unbound_contacts': 53,
 'fnonnat_R': 0.07692307692307693,
 'fnonnat_L': 0.0,
 'fnat_R': 0.8275862068965517,
 'fnat_L': 0.9230769230769231,
 'difficulty': 'Rigid-body',
 'I-RMSD': 1.252618,
 'matched_interface_chains': 2,
 'holo_receptor_interface_res': 29,
 'holo_ligand_interface_res': 13,
 'apo_receptor_interface_res': 26,
 'apo_ligand_interface_res': 12,
 'L-RMSD': 3.9255776,
 'R-RMSD': 0.40761372,
 'unbound_id': 'af__P00761--af__P80424',
 'unbound_body': 'receptor_ligand',
 'monomer_name': 'predicted'}

A bunch of other features of the Structure class are illustrated below

apo_L.atom_array[0:10]

array([
	Atom(np.array([36.778, 16.379, 60.821], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="N", element="N", b_factor=0.0),
	Atom(np.array([37.219, 15.836, 59.542], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([36.18 , 16.079, 58.452], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="C", element="C", b_factor=0.0),
	Atom(np.array([36.532, 16.338, 57.297], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="O", element="O", b_factor=0.0),
	Atom(np.array([37.509, 14.339, 59.666], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CB", element="C", b_factor=0.0),
	Atom(np.array([38.703, 14.01 , 60.548], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CG", element="C", b_factor=0.0),
	Atom(np.array([38.916, 12.517, 60.706], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CD", element="C", b_factor=0.0),
	Atom(np.array([37.981, 11.727, 60.572], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="OE1", element="O", b_factor=0.0),
	Atom(np.array([40.151, 12.123, 60.994], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="NE2", element="N", b_factor=0.0),
	Atom(np.array([34.852, 15.989, 58.853], dtype=float32), chain_id="L", res_id=3, ins_code="", res_name="PRO", hetero=False, atom_name="N", element="N", b_factor=0.0)
])

apo_L.coords[0:10]

array([[36.778, 16.379, 60.821],
       [37.219, 15.836, 59.542],
       [36.18 , 16.079, 58.452],
       [36.532, 16.338, 57.297],
       [37.509, 14.339, 59.666],
       [38.703, 14.01 , 60.548],
       [38.916, 12.517, 60.706],
       [37.981, 11.727, 60.572],
       [40.151, 12.123, 60.994],
       [34.852, 15.989, 58.853]], dtype=float32)

apo_L.residue_names

['ALA',
 'ARG',
 'ASN',
 'ASP',
 'CYS',
 'GLN',
 'GLU',
 'GLY',
 'HIS',
 'ILE',
 'LEU',
 'LYS',
 'MET',
 'PHE',
 'PRO',
 'SER',
 'THR',
 'TRP',
 'VAL']

apo_L.sequence

'QPVNQPILAAAQSLHEATKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPW'

apo_L.atom_array.res_name

array(['GLN', 'GLN', 'GLN', ..., 'TRP', 'TRP', 'TRP'], dtype='<U5')

apo_L.atom_array[apo_L.backbone_mask][0:10]

array([
	Atom(np.array([36.778, 16.379, 60.821], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="N", element="N", b_factor=0.0),
	Atom(np.array([37.219, 15.836, 59.542], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([36.18 , 16.079, 58.452], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="C", element="C", b_factor=0.0),
	Atom(np.array([34.852, 15.989, 58.853], dtype=float32), chain_id="L", res_id=3, ins_code="", res_name="PRO", hetero=False, atom_name="N", element="N", b_factor=0.0),
	Atom(np.array([33.88 , 16.232, 57.771], dtype=float32), chain_id="L", res_id=3, ins_code="", res_name="PRO", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([33.954, 17.664, 57.252], dtype=float32), chain_id="L", res_id=3, ins_code="", res_name="PRO", hetero=False, atom_name="C", element="C", b_factor=0.0),
	Atom(np.array([33.798, 17.833, 55.943], dtype=float32), chain_id="L", res_id=4, ins_code="", res_name="VAL", hetero=False, atom_name="N", element="N", b_factor=0.0),
	Atom(np.array([33.848, 19.155, 55.33 ], dtype=float32), chain_id="L", res_id=4, ins_code="", res_name="VAL", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([32.629, 19.402, 54.448], dtype=float32), chain_id="L", res_id=4, ins_code="", res_name="VAL", hetero=False, atom_name="C", element="C", b_factor=0.0),
	Atom(np.array([32.136, 20.636, 54.462], dtype=float32), chain_id="L", res_id=5, ins_code="", res_name="ASN", hetero=False, atom_name="N", element="N", b_factor=0.0)
])

apo_L.atom_array[apo_L.calpha_mask][0:10]

array([
	Atom(np.array([37.219, 15.836, 59.542], dtype=float32), chain_id="L", res_id=2, ins_code="", res_name="GLN", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([33.88 , 16.232, 57.771], dtype=float32), chain_id="L", res_id=3, ins_code="", res_name="PRO", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([33.848, 19.155, 55.33 ], dtype=float32), chain_id="L", res_id=4, ins_code="", res_name="VAL", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([30.979, 21.004, 53.668], dtype=float32), chain_id="L", res_id=5, ins_code="", res_name="ASN", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([31.94 , 20.151, 50.049], dtype=float32), chain_id="L", res_id=6, ins_code="", res_name="GLN", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([30.278, 23.116, 48.249], dtype=float32), chain_id="L", res_id=7, ins_code="", res_name="PRO", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([32.112, 25.664, 50.491], dtype=float32), chain_id="L", res_id=8, ins_code="", res_name="ILE", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([35.441, 23.864, 49.936], dtype=float32), chain_id="L", res_id=9, ins_code="", res_name="LEU", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([34.772, 23.807, 46.168], dtype=float32), chain_id="L", res_id=10, ins_code="", res_name="ALA", hetero=False, atom_name="CA", element="C", b_factor=0.0),
	Atom(np.array([33.923, 27.56 , 46.154], dtype=float32), chain_id="L", res_id=11, ins_code="", res_name="ALA", hetero=False, atom_name="CA", element="C", b_factor=0.0)
])

apo_L.chain_sequence

{'L': ['Q',
  'P',
  'V',
  'N',
  'Q',
  'P',
  'I',
  'L',
  'A',
  'A',
  'A',
  'Q',
  'S',
  'L',
  'H',
  'E',
  'A',
  'T',
  'K',
  'W',
  'S',
  'S',
  'K',
  'G',
  'N',
  'D',
  'I',
  'I',
  'A',
  'A',
  'A',
  'K',
  'R',
  'M',
  'A',
  'L',
  'L',
  'M',
  'A',
  'E',
  'M',
  'S',
  'R',
  'L',
  'V',
  'R',
  'G',
  'G',
  'S',
  'G',
  'T',
  'K',
  'R',
  'A',
  'L',
  'I',
  'Q',
  'C',
  'A',
  'K',
  'D',
  'I',
  'A',
  'K',
  'A',
  'S',
  'D',
  'E',
  'V',
  'T',
  'R',
  'L',
  'A',
  'K',
  'E',
  'V',
  'A',
  'K',
  'Q',
  'C',
  'T',
  'D',
  'K',
  'R',
  'I',
  'R',
  'T',
  'N',
  'L',
  'L',
  'Q',
  'V',
  'C',
  'E',
  'R',
  'I',
  'P',
  'T',
  'I',
  'S',
  'T',
  'Q',
  'L',
  'K',
  'I',
  'L',
  'S',
  'T',
  'V',
  'K',
  'A',
  'T',
  'M',
  'L',
  'G',
  'R',
  'T',
  'N',
  'I',
  'S',
  'D',
  'E',
  'E',
  'S',
  'E',
  'Q',
  'A',
  'T',
  'E',
  'M',
  'L',
  'V',
  'H',
  'N',
  'A',
  'Q',
  'N',
  'L',
  'M',
  'Q',
  'S',
  'V',
  'K',
  'E',
  'T',
  'V',
  'R',
  'E',
  'A',
  'E',
  'A',
  'A',
  'S',
  'I',
  'K',
  'I',
  'R',
  'T',
  'D',
  'A',
  'G',
  'F',
  'T',
  'L',
  'R',
  'W',
  'V',
  'R',
  'K',
  'T',
  'P',
  'W']}

apo_complex.chain_sequence

{'L': ['Q',
  'P',
  'V',
  'N',
  'Q',
  'P',
  'I',
  'L',
  'A',
  'A',
  'A',
  'Q',
  'S',
  'L',
  'H',
  'E',
  'A',
  'T',
  'K',
  'W',
  'S',
  'S',
  'K',
  'G',
  'N',
  'D',
  'I',
  'I',
  'A',
  'A',
  'A',
  'K',
  'R',
  'M',
  'A',
  'L',
  'L',
  'M',
  'A',
  'E',
  'M',
  'S',
  'R',
  'L',
  'V',
  'R',
  'G',
  'G',
  'S',
  'G',
  'T',
  'K',
  'R',
  'A',
  'L',
  'I',
  'Q',
  'C',
  'A',
  'K',
  'D',
  'I',
  'A',
  'K',
  'A',
  'S',
  'D',
  'E',
  'V',
  'T',
  'R',
  'L',
  'A',
  'K',
  'E',
  'V',
  'A',
  'K',
  'Q',
  'C',
  'T',
  'D',
  'K',
  'R',
  'I',
  'R',
  'T',
  'N',
  'L',
  'L',
  'Q',
  'V',
  'C',
  'E',
  'R',
  'I',
  'P',
  'T',
  'I',
  'S',
  'T',
  'Q',
  'L',
  'K',
  'I',
  'L',
  'S',
  'T',
  'V',
  'K',
  'A',
  'T',
  'M',
  'L',
  'G',
  'R',
  'T',
  'N',
  'I',
  'S',
  'D',
  'E',
  'E',
  'S',
  'E',
  'Q',
  'A',
  'T',
  'E',
  'M',
  'L',
  'V',
  'H',
  'N',
  'A',
  'Q',
  'N',
  'L',
  'M',
  'Q',
  'S',
  'V',
  'K',
  'E',
  'T',
  'V',
  'R',
  'E',
  'A',
  'E',
  'A',
  'A',
  'S',
  'I',
  'K',
  'I',
  'R',
  'T',
  'D',
  'A',
  'G',
  'F',
  'T',
  'L',
  'R',
  'W',
  'V',
  'R',
  'K',
  'T',
  'P',
  'W'],
 'R': ['H',
  'M',
  'L',
  'D',
  'P',
  'E',
  'E',
  'I',
  'R',
  'K',
  'R',
  'L',
  'E',
  'H',
  'T',
  'E',
  'R',
  'Q',
  'F',
  'R',
  'N',
  'R',
  'R',
  'K',
  'I',
  'L',
  'I',
  'R',
  'G',
  'L',
  'P',
  'G',
  'D',
  'V',
  'T',
  'N',
  'Q',
  'E',
  'V',
  'H',
  'D',
  'L',
  'L',
  'S',
  'D',
  'Y',
  'E',
  'L',
  'K',
  'Y',
  'C',
  'F',
  'V',
  'D',
  'K',
  'Y',
  'K',
  'G',
  'T',
  'A',
  'F',
  'V',
  'T',
  'L',
  'L',
  'N',
  'G',
  'E',
  'Q',
  'A',
  'E',
  'A',
  'A',
  'I',
  'N',
  'A',
  'F',
  'H',
  'Q',
  'S',
  'R',
  'L',
  'R',
  'E',
  'R',
  'E',
  'L',
  'S',
  'V',
  'Q',
  'L',
  'Q',
  'P',
  'T',
  'D',
  'A',
  'L',
  'L',
  'C',
  'V',
  'A',
  'N',
  'L',
  'P',
  'P',
  'S',
  'L',
  'T',
  'Q',
  'Q',
  'Q',
  'F',
  'E',
  'E',
  'L',
  'V',
  'R',
  'P',
  'F',
  'G',
  'S',
  'L',
  'E',
  'R',
  'C',
  'F',
  'L',
  'V',
  'Y',
  'S',
  'E',
  'R',
  'T',
  'G',
  'Q',
  'S',
  'K',
  'G',
  'Y',
  'G',
  'F',
  'A',
  'E',
  'Y',
  'M',
  'K',
  'K',
  'D',
  'S',
  'A',
  'A',
  'R',
  'A',
  'K',
  'S',
  'D',
  'L',
  'L',
  'G',
  'K',
  'P',
  'L',
  'G',
  'P',
  'R',
  'T',
  'L',
  'Y',
  'V',
  'H',
  'W',
  'T',
  'D',
  'A',
  'G',
  'Q',
  'L',
  'T',
  'P',
  'A',
  'L',
  'L',
  'H',
  'S',
  'R',
  'C',
  'L',
  'C',
  'V',
  'D',
  'R',
  'L',
  'P',
  'P',
  'G',
  'F',
  'N',
  'D',
  'V',
  'D',
  'A',
  'L',
  'C',
  'R',
  'A',
  'L',
  'S',
  'A',
  'V',
  'H',
  'S',
  'P',
  'T',
  'F',
  'C',
  'Q',
  'L',
  'A',
  'C',
  'G',
  'Q',
  'D',
  'G',
  'Q',
  'L',
  'K',
  'G',
  'F',
  'A',
  'V',
  'L',
  'E',
  'Y',
  'E',
  'T',
  'A',
  'E',
  'M',
  'A',
  'E',
  'E',
  'A',
  'Q',
  'Q',
  'Q',
  'A',
  'D',
  'G',
  'L',
  'S',
  'L',
  'G',
  'G',
  'S',
  'H',
  'L',
  'R',
  'V',
  'S',
  'F',
  'C',
  'A',
  'P',
  'G',
  'P',
  'P',
  'G',
  'R',
  'S',
  'M',
  'L',
  'A',
  'A',
  'L',
  'I',
  'A',
  'A',
  'Q',
  'A',
  'T']}

apo_L.sequence

'QPVNQPILAAAQSLHEATKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPW'