Research workbench
Crystal structure of mitochondrial cytochrome BC1 in complex with antimycin A1
Analyse Crystal structure of mitochondrial cytochrome BC1 in complex with antimycin A1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NTK
- Type
- protein
- Length
- 2,114 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552
- Ligands
- HEM, AY1, FES
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial (EC 1.10.2.2) | protein | 446 | 46% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 423 | 46% helix, 20% strand | P23004 |
| C | Cytochrome B | protein | 378 | 70% helix, 2% strand | P00157 |
| D | Cytochrome C1 | protein | 241 | 42% helix, 6% strand | P00125 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (EC 1.10.2.2) | protein | 196 | 30% helix, 22% strand | P13272 |
| F | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 105 | 69% helix, 0% strand | P00129 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 79 | 52% helix, 9% strand | P13271 |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 76 | 76% helix, 0% strand | P00126 |
| I | Ubiquinol-cytochrome C reductase 8 kda protein (EC 1.10.2.2) | protein | 57 | 12% helix, 11% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 60 | 72% helix, 0% strand | P00130 |
| K | Ubiquinol-cytochrome C reductase complex 6.4 kda protein (EC 1.10.2.2) | protein | 53 | 60% helix, 0% strand | P07552 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, D
- AY1 · [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 2-methylpropanoate · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
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 | 793 | 0.83 | 0.86 | 88 | HEM |
| 2 | 969 | 0.83 | 0.85 | 102 | empty |
| 3 | 872 | 0.83 | 0.85 | 96 | empty |
| 4 | 613 | 0.80 | 0.85 | 53 | empty |
| 5 | 494 | 0.80 | 0.86 | 52 | HEM, AY1 |
Interfaces
24 interfaces between chains.
- A–B · 2198 Ų buried · 38 hydrogen bonds · protein-protein
- B–I · 1955 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1681 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 1523 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1266 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1NTK · Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1 · the same entry in another collection · chain K against K, 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
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 1NTK · PDBe 1NTK · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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