Research workbench
Cytochrome BC1 complex from chicken
Analyse Cytochrome BC1 complex from chicken in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BCC
- Type
- protein
- Length
- 2,000 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol cytochrome C oxidoreductase
- EC
- 1.10.2.2
- UniProt
- P13272, P23004, P18946, P00125, P00129, P13271, P00126, P00130
- Ligands
- HEM, PEE, U10, FES
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 10 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 442 | 45% helix, 19% strand | P13272 |
| B | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 406 | 44% helix, 19% strand | P23004 |
| C | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 379 | 66% helix, 2% strand | P18946 |
| D | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 241 | 39% helix, 7% strand | P00125 |
| E | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 196 | 30% helix, 23% strand | P13272 |
| F | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 100 | 67% helix, 0% strand | P00129 |
| G | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 78 | 49% helix, 10% strand | P13271 |
| H | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 66 | 73% helix, 0% strand | P00126 |
| I | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 33 | 0% helix, 0% strand | — |
| J | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 59 | 80% helix, 0% strand | P00130 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, D
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains C, F, G, A, D, E, J
- U10 · Ubiquinone-10 · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
- BOG · octyl beta-D-glucopyranoside · additive · chains C, D, E, J
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.86 | 0.92 | 57 | HEM |
| 2 | 869 | 0.82 | 0.84 | 102 | empty |
| 3 | 160 | 0.81 | 0.97 | 27 | empty |
| 4 | 781 | 0.80 | 0.83 | 85 | HEM, U10 |
| 5 | 865 | 0.79 | 0.81 | 63 | PEE |
Interfaces
22 interfaces between chains.
- C–D · 1601 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1446 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1236 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 1174 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1041 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 cofactor (disulfide, heme attachment).
Compared structures
- 1BCC · Cytochrome BC1 complex from chicken · the same entry in another collection · chain J against J, TM-score 1.00
- P18946 · AlphaFold monomer V2.0 prediction for cytochrome B (P18946) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P23004 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 2, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P23004
- Every structure of UniProt P18946
- 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 1BCC · PDBe 1BCC · UniProt P13272 · UniProt P23004 · UniProt P18946 · UniProt P00125 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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