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Cryoem structure of bovine cytochrome BC1 in complex with the anti- malarial compound GSK932121

Analyse Cryoem structure of bovine cytochrome BC1 in complex with the anti- malarial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FO0
Type: protein
Length: 3,910 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
EC: 1.10.2.2
UniProt: P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130
Ligands: HEM, G8U, HEC
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N, A	Cytochrome B-C1 complex subunit 1, mitochondrial	protein	443	45% helix, 19% strand	P31800
O, B	Cytochrome B-C1 complex subunit 2, mitochondrial	protein	414	40% helix, 18% strand	P23004
P, C	Cytochrome B	protein	370	71% helix, 1% strand	P00157
Q, D	Cytochrome C1, heme protein, mitochondrial	protein	239	40% helix, 8% strand	P00125
R, E	Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2)	protein	178	28% helix, 15% strand	P13272
S, F	Cytochrome B-C1 complex subunit 7	protein	98	59% helix, 0% strand	P00129
T, G	Cytochrome B-C1 complex subunit 8	protein	74	47% helix, 9% strand	P13271
U, H	Cytochrome B-C1 complex subunit 6, mitochondrial	protein	65	74% helix, 0% strand	P00126
V, I	Chain I/V	protein	17	0% helix, 47% strand	—
W, J	Cytochrome B-C1 complex subunit 9	protein	57	77% helix, 0% strand	P00130

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains P, C
G8U · 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol · ligand · 2 copies · chains P, C
HEC · Heme C · ligand · 2 copies · chains Q, D

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	387	0.85	0.93	50	HEM
2	401	0.84	0.92	49	HEM
3	197	0.82	0.96	29	empty
4	1098	0.82	0.83	98	empty
5	190	0.82	0.96	28	empty

Interfaces

55 interfaces between chains.

N–O · 2122 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2099 Å² buried · 41 hydrogen bonds · protein-protein
P–Q · 1719 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1707 Å² buried · 16 hydrogen bonds · protein-protein
P–S · 1207 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6FO0 · CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial compound… · the same entry in another collection · chain W against W, 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
Elsewhere: RCSB PDB 6FO0 · PDBe 6FO0 · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130

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