MolNFT v1 · #154851 · protein
X-ray structure of the proton-pumping cytochrome AA3-600 menaquinol oxidase from bacillus subtilis
6KOE · AA3-600 quinol oxidase subunit I: “X-ray structure of the proton-pumping cytochrome AA3-600 menaquinol oxidase from bacillus subtilis”. X-ray diffraction, 3 ligands (HEA, HQO, CU), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 6KOE
- Type
- protein
- Length
- 2,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AA3-600 quinol oxidase subunit I; Quinol oxidase subunit 2; AA3-600 quinol oxidase…
- EC
- 1.10.3.-
- UniProt
- A0A063X8D0, A0A2I7T8S1, A0A063X6N5, P34959
- Ligands
- HEA, HQO, CU
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | AA3-600 quinol oxidase subunit I | protein | 607 | 58% helix, 0% strand | A0A063X8D0 |
| B, F | Quinol oxidase subunit 2 (EC 1.10.3.-) | protein | 256 | 21% helix, 18% strand | A0A2I7T8S1 |
| C, G | AA3-600 quinol oxidase subunit iiii | protein | 178 | 69% helix, 0% strand | A0A063X6N5 |
| D, H | AA3-600 quinol oxidase subunit IV | protein | 70 | 69% helix, 0% strand | P34959 |
Ligands and binding sites
- HEA · Heme-A · ligand · 4 copies · chains A, B, E, F
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · 2 copies · chains A, E
- CU · Copper (II) ion · metal · 2 copies · chains A, E
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 | 1196 | 0.89 | 0.90 | 105 | HEA |
| 2 | 1189 | 0.89 | 0.90 | 102 | HEA |
| 3 | 1041 | 0.85 | 0.86 | 106 | HQO |
| 4 | 878 | 0.83 | 0.84 | 63 | empty |
| 5 | 1044 | 0.82 | 0.83 | 109 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3274 Ų buried · 22 hydrogen bonds · protein-protein
- F–E · 3246 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1519 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 1453 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6KOE · X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus… · the same entry in another collection · chain E against E, TM-score 1.00
- P34959 · AlphaFold monomer V2.0 prediction for quinol oxidase subunit 4 (P34959) · a predicted model of the same protein · chain D against A, TM-score 0.59
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 A0A063X8D0
- Every structure of UniProt A0A2I7T8S1
- Every structure of UniProt A0A063X6N5
- Every structure of UniProt P34959
- Elsewhere: RCSB PDB 6KOE · PDBe 6KOE · UniProt A0A063X8D0 · UniProt A0A2I7T8S1 · UniProt A0A063X6N5 · UniProt P34959
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