MolNFT v1 · #173243 · protein
Cytochrome C oxidase structure in R-state
7ATN · Cytochrome C oxidase subunit 1-beta: “Cytochrome C oxidase structure in R-state”. Electron microscopy, 6 ligands (HEA, CUA, PC1), 10 pockets (best druggability 0.90). MolNFT v1 #173243 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7ATN
- Type
- protein
- Length
- 1,098 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, CUA, PC1, MN, CU, CA
- Pockets
- 10 · best druggability 0.90
Structure
electron microscopy · 4 distinct chains · 63% 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 | 68% helix, 2% strand | P98002 |
| B | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 252 | 38% helix, 25% strand | P08306 |
| C | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 269 | 72% helix, 2% strand | P06030 |
| D | Cytochrome C oxidase subunit 4 (EC 7.1.1.9) | protein | 40 | 80% helix, 0% strand | P77921 |
Ligands and binding sites
- HEA · Heme-A · ligand · 2 copies · chains A, B
- CUA · Dinuclear copper ion · ligand · chains B
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains C
- MN · Manganese (II) ion · metal · chains A, B
- CU · Copper (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.90 | 0.92 | 117 | HEA, CU |
| 2 | 1183 | 0.82 | 0.83 | 83 | PC1 |
| 3 | 937 | 0.79 | 0.80 | 75 | empty |
| 4 | 208 | 0.58 | 0.80 | 24 | empty |
| 5 | 133 | 0.49 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3949 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2731 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 653 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 265 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7ATN · Cytochrome c oxidase structure in R-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
- 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
- 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
- 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 0.93
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 7ATN · PDBe 7ATN · UniProt P98002 · UniProt P08306 · UniProt P06030 · UniProt P77921
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