MolNFT v2 · #214985 · protein
Serial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase without pump laser irradiation
8K65 · Cytochrome c oxidase subunit 1: “Serial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase without pump laser…”. X-ray diffraction at 2, 5 ligands (HEM, HAS, CUA), 6 pockets (best druggability 0.90).…
- PDB
- 8K65
- Type
- protein
- Length
- 752 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Thermus thermophilus HB8
- Molecule
- Cytochrome c oxidase subunit 1; Cytochrome c oxidase subunit 2; Cytochrome c oxidase…
- EC
- 7.1.1.9
- UniProt
- Q5SJ79, Q5SJ80, P82543
- Ligands
- HEM, HAS, CUA, CU, CMO
- Pockets
- 6 · best druggability 0.90
Structure
x-ray diffraction · resolution 2 · 3 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome c oxidase subunit 1 (EC 7.1.1.9) | protein | 554 | 74% helix, 2% strand | Q5SJ79 |
| B | Cytochrome c oxidase subunit 2 (EC 7.1.1.9) | protein | 167 | 27% helix, 35% strand | Q5SJ80 |
| C | Cytochrome c oxidase polypeptide 2A (EC 7.1.1.9) | protein | 31 | 87% helix, 0% strand | P82543 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HAS · Heme-as · ligand · chains A, C
- CUA · Dinuclear copper ion · ligand · chains B
- CU · Copper (II) ion · metal · chains A
- CMO · Carbon monoxide · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.90 | 0.91 | 141 | HEM, HAS, CMO |
| 2 | 53 | 0.68 | 0.96 | 18 | empty |
| 3 | 105 | 0.36 | 0.73 | 17 | empty |
| 4 | 73 | 0.33 | 0.75 | 18 | empty |
| 5 | 58 | 0.30 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2923 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1024 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- Q5SJ79 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (Q5SJ79) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q5SJ80 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (Q5SJ80) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P82543 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase polypeptide 2A (P82543) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q5SJ79
- Every structure of UniProt Q5SJ80
- Every structure of UniProt P82543
- Elsewhere: RCSB PDB 8K65 · PDBe 8K65 · UniProt Q5SJ79 · UniProt Q5SJ80 · UniProt P82543
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