Research workbench
Crystal structure of bovine cytochrome BC1 in complex with quinolone inhibitor RKA066
Analyse Crystal structure of bovine cytochrome BC1 in complex with quinolone inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZFU
- Type
- protein
- Length
- 2,015 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
- 7.1.1.8
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130
- Ligands
- CDL, HEM, PEE, 6PE, JHE, HEC, FES, PX4, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 444 | 46% helix, 19% strand | P31800 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 415 | 46% helix, 20% strand | P23004 |
| C | Cytochrome B | protein | 378 | 69% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 239 | 40% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 196 | 32% helix, 18% strand | P13272 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 99 | 70% 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 7.1.1.8) | 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
- JHE · 3-methyl-1-oxidanyl-2-[4-[[4-(trifluoromethyloxy) phenyl]methyl]phenyl]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 · 5 copies · chains D, F, G
- 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 | 383 | 0.84 | 0.93 | 44 | HEM |
| 2 | 1163 | 0.84 | 0.85 | 132 | empty |
| 3 | 818 | 0.82 | 0.85 | 87 | empty |
| 4 | 839 | 0.80 | 0.83 | 71 | PEE, PO4 |
| 5 | 469 | 0.79 | 0.86 | 48 | HEM, JHE |
Interfaces
22 interfaces between chains.
- A–B · 2105 Ų buried · 45 hydrogen bonds · protein-protein
- B–I · 1654 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1646 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 1215 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 1182 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6ZFU · Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor RKA066 · 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 6ZFU · PDBe 6ZFU · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.