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Cryoem structure of bovine cytochrome BC1 in complex with the anti- malarial inhibitor SCR0911

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: 6FO6
Type: protein
Length: 3,868 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B-C1 complex subunit rieske, mitochondrial; Cytochrome B-C1 complex subunit 1…
EC: 1.10.2.2
UniProt: P13272, P31800, P23004, P00157, P00125, P00129, P13271, P00126, P00130
Ligands: HEM, DY2, HEC
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 11 distinct chains · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, R	Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2)	protein	178	30% helix, 13% strand	P13272
A, N	Cytochrome B-C1 complex subunit 1, mitochondrial	protein	444	45% helix, 18% strand	P31800
B	Cytochrome B-C1 complex subunit 2, mitochondrial	protein	414	44% helix, 20% strand	P23004
C, P	Cytochrome B	protein	370	68% helix, 1% strand	P00157
D, Q	Cytochrome C1, heme protein, mitochondrial	protein	237	38% helix, 9% strand	P00125
F, S	Cytochrome B-C1 complex subunit 7	protein	98	65% helix, 0% strand	P00129
G, T	Cytochrome B-C1 complex subunit 8	protein	72	53% helix, 13% strand	P13271
H, U	Cytochrome B-C1 complex subunit 6, mitochondrial	protein	65	72% helix, 0% strand	P00126
J	Cytochrome B-C1 complex subunit 9	protein	58	83% helix, 0% strand	P00130
O	Cytochrome B-C1 complex subunit 2, mitochondrial	protein	411	44% helix, 20% strand	P23004
W	Cytochrome B-C1 complex subunit 9	protein	57	79% helix, 0% strand	P00130

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
DY2 · 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy) phenyl]pyridin-3-yl]quinolin-4-ol · ligand · 2 copies · chains C, P
HEC · Heme C · ligand · 2 copies · chains D, 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	725	0.83	0.86	69	HEM
2	694	0.83	0.87	69	HEM
3	629	0.82	0.87	66	empty
4	1063	0.82	0.83	108	empty
5	672	0.81	0.85	95	empty

Interfaces

51 interfaces between chains.

N–O · 2045 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 2043 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 1714 Å² buried · 19 hydrogen bonds · protein-protein
P–Q · 1706 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 1211 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6FO6 · CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial inhibitor… · the same entry in another collection · chain N against N, 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 P13272
Every structure of UniProt P31800
Every structure of UniProt P23004
Every structure of UniProt P00157
Every structure of UniProt P00125
Every structure of UniProt P00129
Every structure of UniProt P13271
Every structure of UniProt P00126
Every structure of UniProt P00130
Elsewhere: RCSB PDB 6FO6 · PDBe 6FO6 · UniProt P13272 · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130

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