MolNFT v1 · #1934 · protein

Cytochrome BC1 complex from bovine

1BGY: “Cytochrome BC1 complex from bovine”. X-ray diffraction, 3 ligands (HEM, HEC, FES), 20 pockets (best druggability 0.88). MolNFT v1 #1934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1BGY
Type: protein
Length: 3,977 residues
Chains: 22
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome BC1 complex
EC: 1.10.2.2
UniProt: P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552
Ligands: HEM, HEC, FES
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 12 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M	Cytochrome BC1 complex (EC 1.10.2.2)	protein	446	46% helix, 16% strand	P31800
B, N	Cytochrome BC1 complex (EC 1.10.2.2)	protein	419	46% helix, 16% strand	P23004
C, O	Cytochrome BC1 complex (EC 1.10.2.2)	protein	379	69% helix, 2% strand	P00157
D, P	Cytochrome BC1 complex (EC 1.10.2.2)	protein	241	41% helix, 3% strand	P00125
E	Cytochrome BC1 complex (EC 1.10.2.2)	protein	75	59% helix, 1% strand	P13272
F, R	Cytochrome BC1 complex (EC 1.10.2.2)	protein	106	67% helix, 0% strand	P00129
G, S	Cytochrome BC1 complex (EC 1.10.2.2)	protein	81	57% helix, 9% strand	P13271
H, T	Cytochrome BC1 complex (EC 1.10.2.2)	protein	64	78% helix, 0% strand	P00126
I, U	Cytochrome BC1 complex (EC 1.10.2.2)	protein	33	0% helix, 21% strand	P13272
J, V	Cytochrome BC1 complex (EC 1.10.2.2)	protein	62	69% helix, 0% strand	P00130
K, W	Cytochrome BC1 complex (EC 1.10.2.2)	protein	22	86% helix, 0% strand	P07552
Q	Cytochrome BC1 complex (EC 1.10.2.2)	protein	196	32% helix, 18% strand	P13272

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, O
HEC · Heme C · ligand · 2 copies · chains D, P
FES · Fe2/s2 (inorganic) cluster · ligand · chains Q

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	527	0.88	0.94	63	HEM
2	528	0.87	0.93	65	HEM
3	844	0.85	0.87	94	empty
4	836	0.84	0.86	96	empty
5	928	0.84	0.85	88	empty

Interfaces

61 interfaces between chains.

M–N · 2095 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2087 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1645 Å² buried · 17 hydrogen bonds · protein-protein
O–P · 1643 Å² buried · 18 hydrogen bonds · protein-protein
N–U · 1561 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 4 cofactor (disulfide, heme c attachment).

Compared structures

1BGY · Cytochrome BC1 complex from bovine · the same entry in another collection · chain G against G, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P31800
Every structure of UniProt P23004
Every structure of UniProt P00157
Every structure of UniProt P00125
Every structure of UniProt P13272
Every structure of UniProt P00129
Every structure of UniProt P13271
Every structure of UniProt P00126
Every structure of UniProt P00130
Every structure of UniProt P07552
Elsewhere: RCSB PDB 1BGY · PDBe 1BGY · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552

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