MolNFT v1 · #154848 · protein
X-ray structure of the proton-pumping cytochrome AA3-600 menaquinol oxidase from bacillus subtilis
6KOB · 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, MQ7, CU), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 6KOB
- 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, MQ7, 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 | 71% helix, 0% strand | A0A063X6N5 |
| D, H | AA3-600 quinol oxidase subunit IV,QUINOL oxidase subunit 4 (EC 1.10.3.-) | protein | 70 | 70% helix, 0% strand | P34959 |
Ligands and binding sites
- HEA · Heme-A · ligand · 4 copies · chains A, B, E, F
- MQ7 · Menaquinone-7 · 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 | 1197 | 0.89 | 0.90 | 105 | HEA |
| 2 | 1122 | 0.89 | 0.90 | 101 | HEA |
| 3 | 936 | 0.84 | 0.86 | 99 | empty |
| 4 | 974 | 0.84 | 0.86 | 95 | empty |
| 5 | 1004 | 0.82 | 0.83 | 84 | empty |
Interfaces
13 interfaces between chains.
- F–E · 3304 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3292 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1511 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 1473 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1427 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6KOB · 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 0.58
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 6KOB · PDBe 6KOB · UniProt A0A063X8D0 · UniProt A0A2I7T8S1 · UniProt A0A063X6N5 · UniProt P34959
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