Research workbench
Cytochrome C oxidase structure in O-state
Analyse Cytochrome C oxidase structure in O-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AU6
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1-beta; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 7.1.1.9
- UniProt
- P98002, P08306, P06030, P77921
- Ligands
- HEA, PC1, PEO, CUA, CU, CA, MN, OXY
- Pockets
- 9 · best druggability 0.90
Structure
electron microscopy · 4 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1-beta (EC 7.1.1.9) | protein | 537 | 70% helix, 2% strand | P98002 |
| B | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 248 | 38% helix, 26% strand | P08306 |
| C | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 269 | 71% helix, 1% strand | P06030 |
| D | Cytochrome C oxidase subunit 4 (EC 7.1.1.9) | protein | 38 | 84% helix, 0% strand | P77921 |
Ligands and binding sites
- HEA · Heme-A · ligand · 2 copies · chains A, B
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, C, D
- PEO · Hydrogen peroxide · ligand · chains A
- CUA · Dinuclear copper ion · ligand · chains B
- CU · Copper (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A, B
- OXY · Oxygen molecule · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.90 | 0.92 | 111 | HEA, OXY, PEO |
| 2 | 902 | 0.83 | 0.85 | 77 | PC1 |
| 3 | 911 | 0.78 | 0.80 | 71 | PC1 |
| 4 | 211 | 0.58 | 0.80 | 23 | empty |
| 5 | 128 | 0.50 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3907 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2794 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 592 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 296 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7AU6 · Cytochrome c oxidase structure in O-state · the same entry in another collection · chain D against D, TM-score 1.00
- P98002 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1-beta (P98002) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P08306 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P08306) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P06030 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 3 (P06030) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P77921 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 4 (P77921) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P98002
- Every structure of UniProt P08306
- Every structure of UniProt P06030
- Every structure of UniProt P77921
- Elsewhere: RCSB PDB 7AU6 · PDBe 7AU6 · UniProt P98002 · UniProt P08306 · UniProt P06030 · UniProt P77921
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