Research workbench
Stigmatellin-bound cytochrome BC1 complex from chicken
Analyse Stigmatellin-bound 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
- 2BCC
- 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
- P18946
- Ligands
- HEM, PEE, U10, SIG, FES
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 10 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 442 | 45% helix, 17% strand | — |
| B | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 406 | 41% helix, 17% strand | — |
| 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 | 40% helix, 7% strand | — |
| E | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 196 | 26% helix, 19% strand | — |
| F | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 100 | 69% helix, 0% strand | — |
| G | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 78 | 46% helix, 10% strand | — |
| H | Ubiquinol cytochrome C oxidoreductase (EC 1.10.2.2) | protein | 66 | 71% helix, 0% strand | — |
| 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 | 73% helix, 0% strand | — |
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
- SIG · Stigmatellin · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.86 | 0.93 | 62 | HEM |
| 2 | 975 | 0.80 | 0.82 | 91 | empty |
| 3 | 705 | 0.80 | 0.84 | 80 | empty |
| 4 | 467 | 0.79 | 0.86 | 49 | HEM, U10 |
| 5 | 858 | 0.79 | 0.81 | 60 | PEE |
Interfaces
22 interfaces between chains.
- C–D · 1635 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1234 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 1173 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1076 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 cofactor (disulfide, heme attachment).
Compared structures
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 P18946
- Elsewhere: RCSB PDB 2BCC · PDBe 2BCC · UniProt P18946
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