MolNFT v1 · #129437 · protein
Crystal structure of bovine cytochrome BC1 in complex with inhibitor SCR0911.
5OKD · Cytochrome B-C1 complex subunit 1, mitochondrial: “Crystal structure of bovine cytochrome BC1 in complex with inhibitor SCR0911.”. X-ray diffraction, 9 ligands (CDL, HEM, PEE), 20 pockets (best druggability 0.85). MolNFT v1 #129437…
- PDB
- 5OKD
- Type
- protein
- Length
- 2,016 residues
- Chains
- 10
- Method
- x-ray diffraction
- 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
- CDL, HEM, PEE, 6PE, 9XE, HEC, FES, PX4, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 10 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 445 | 47% helix, 19% strand | P31800 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 415 | 47% helix, 20% strand | P23004 |
| C | Cytochrome B | protein | 378 | 70% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 239 | 40% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 32% helix, 20% strand | P13272 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 99 | 67% helix, 1% strand | P00129 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 74 | 51% helix, 12% strand | P13271 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 65 | 75% helix, 0% strand | P00126 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 46 | 9% helix, 17% strand | P13272 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 59 | 81% helix, 0% strand | P00130 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 4 copies · chains A, C, F, G, D, E, J
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains C
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains C, F, G, D, E, J
- 6PE · 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine · ligand · chains A, C, D
- 9XE · 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy) phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one · ligand · chains C
- HEC · Heme C · ligand · chains D
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · chains A, C, D, E, J
- PO4 · Phosphate ion · ion · 6 copies · chains D, E, G, F
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C
- LMT · Dodecyl-beta-D-maltoside · additive · chains C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.85 | 0.93 | 41 | HEM |
| 2 | 858 | 0.83 | 0.85 | 101 | empty |
| 3 | 886 | 0.82 | 0.84 | 94 | 6PE, CDL, PX4, PO4 |
| 4 | 1022 | 0.82 | 0.83 | 87 | empty |
| 5 | 648 | 0.79 | 0.84 | 59 | PEE |
Interfaces
22 interfaces between chains.
- A–B · 2133 Ų buried · 44 hydrogen bonds · protein-protein
- B–I · 1776 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1735 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1223 Ų buried · 11 hydrogen bonds · protein-protein
- A–I · 1176 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5OKD · Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911. · the same entry in another collection · chain J against J, TM-score 1.00
- P00157 · AlphaFold monomer V2.0 prediction for cytochrome B (P00157) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P31800 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 1, mitochondrial… · a predicted model of the same protein · chain A against A, 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 5OKD · PDBe 5OKD · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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