Retrieve Bound Molecule Data From PDBe

[NatureGeorge]

Get Bound Molecules for a PDB Entry

• Provided by PDBe Graph API
• Calculated by arpeggio
• bm is denoted as bound molecules
• bm_id (Bound molecule ID) is the identifier of a bound molecule instance

注意: PDBe目前采取BiologicalUnit来提供Bound Molecule信息,但没指出是哪个BiologicalUnit; 可以依据residue_number & struct_asym_id来去重; 但对于BiologicalUnit是AsymmetricUnit的子集的情况，PDBe目前没给出AsymmetricUnit里所有的配体，只给该BiologicalUnit有的

ob = PDB('2jfs')
bm_df = ob.get_bound_molecules().result()
bm_df
# NOTE: bound molecules can either be ion or other molecules, you can check molecule_name & chem_comp_id

click to view dataframe

	bm_id	pdb_id	chain_id	author_residue_number	chem_comp_id	author_insertion_code	entity_id	molecule_type	chain_id_suffix	multiple_conformers	observed_ratio	residue_name	residue_number	struct_asym_id	molecule_name
0	bm1	2jfs	A	1234	MN		2	bound	1	NaN	1	MN	1	B	["MANGANESE (II) ION"]
1	bm2	2jfs	A	1235	MN		2	bound	1	NaN	1	MN	1	C	["MANGANESE (II) ION"]
2	bm3	2jfs	A	1236	MN		2	bound	1	NaN	1	MN	1	D	["MANGANESE (II) ION"]
3	bm4	2jfs	A	1237	CAC		3	bound	1	NaN	1	CAC	1	E	["CACODYLATE ION"]
4	bm5	2jfs	A	1238	GOL		4	bound	1	NaN	1	GOL	1	F	["GLYCEROL"]
5	bm6	2jfs	A	1239	GOL		4	bound	1	NaN	1	GOL	1	G	["GLYCEROL"]
6	bm7	2jfs	A	1240	GOL		4	bound	1	NaN	1	GOL	1	H	["GLYCEROL"]

Get Bound Molecule Interaction Info

Noted that the target bound molecule can not only interact with amino acids, but also can interact with other molecule

# Assume that we only focus on Mn ion for PDB('2jfs')
bm_ids = bm_df[bm_df.chem_comp_id.str.startswith('MN')].bm_id
concat([ob.get_bound_molecule_interaction(bm_id).result() for bm_id in bm_ids], sort=False, ignore_index=True)

click to view dataframe

	chain_id	chain_id_suffix	residue_name	author_residue_number	author_insertion_code	bm_id	entity_id	multiple_conformers	observed_ratio	pdb_id	residue_number	struct_asym_id	molecule_type	molecule_name
0	A	1	MN	1235		bm1	2	NaN	1	2jfs	1	C	bound	["MANGANESE (II) ION"]
1	A	1	CAC	1237		bm1	3	NaN	1	2jfs	1	E	bound	["CACODYLATE ION"]
2	A	1	ASP	35		bm1	1	NaN	1	2jfs	36	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
3	A	1	GLY	36		bm1	1	NaN	1	2jfs	37	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
4	A	1	MN	1235		bm2	2	NaN	1	2jfs	1	C	bound	["MANGANESE (II) ION"]
5	A	1	MN	1235		bm2	2	NaN	1	2jfs	1	C	bound	["MANGANESE (II) ION"]
6	A	1	CAC	1237		bm2	3	NaN	1	2jfs	1	E	bound	["CACODYLATE ION"]
7	A	1	ASP	185		bm2	1	NaN	1	2jfs	186	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
8	A	1	ASP	223		bm2	1	NaN	1	2jfs	224	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
9	A	1	ASP	35		bm2	1	NaN	1	2jfs	36	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
10	A	1	MN	1235		bm3	2	NaN	1	2jfs	1	C	bound	["MANGANESE (II) ION"]
11	A	1	CAC	1237		bm3	3	NaN	1	2jfs	1	E	bound	["CACODYLATE ION"]
12	A	1	HIS	153		bm3	1	NaN	1	2jfs	154	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...
13	A	1	ASP	185		bm3	1	NaN	1	2jfs	186	A	polypeptide(L)	["PPM-type phosphatase domain-containing prote...

Get Bound Molecules for Many PDB Entries

bm_dfs = PDBs(['2jfs', '1ga7', '4wd0', '1a01']).fetch('get_bound_molecules').run(tqdm).result()
bm_df = concat(bm_dfs, sort=False, ignore_index=True)