Research workbench
X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis complexed with 3-iodo-N-oxo-2-heptyl-4-hydroxyquinoline
Analyse X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KOC
- Type
- protein
- Length
- 2,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Bacillus subtilis; Bacillus subtilis (strain 168); Bacillus subtilis subsp.…
- 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, IHQ, CU
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 3.8 · 4 distinct chains · 53% 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 | 72% helix, 0% strand | A0A063X6N5 |
| D, H | Quinol oxidase subunit 4,Quinol oxidase subunit 4 (EC 1.10.3.-) | protein | 70 | 73% helix, 0% strand | P34959 |
Ligands and binding sites
- HEA · Heme-A · ligand · 4 copies · chains A, B, E, F
- IHQ · 2-heptyl-3-iodanyl-1-oxidanyl-quinolin-4-one · 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 | 1179 | 0.89 | 0.90 | 102 | HEA |
| 2 | 1194 | 0.89 | 0.90 | 108 | HEA |
| 3 | 1062 | 0.85 | 0.86 | 120 | IHQ |
| 4 | 934 | 0.84 | 0.86 | 105 | IHQ |
| 5 | 823 | 0.83 | 0.85 | 61 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3319 Ų buried · 22 hydrogen bonds · protein-protein
- F–E · 3287 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1516 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1491 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1435 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6KOC · X-ray structure of the proton-pumping cytochrome AA3-600 menaquinol oxidase from bacillus… · the same entry in another collection · chain H against H, 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 6KOC · PDBe 6KOC · UniProt A0A063X8D0 · UniProt A0A2I7T8S1 · UniProt A0A063X6N5 · UniProt P34959
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.