MolNFT v2 · #117087 · protein
The structure of bd oxidase from Geobacillus thermodenitrificans
5DOQ · Bd-type quinol oxidase subunit I: “The structure of bd oxidase from Geobacillus thermodenitrificans”. X-ray diffraction at 3.05, 2 ligands (HEB, HDD), 9 pockets (best druggability 0.90). MolNFT v2 #117087 on GenesisL1: 3D structure…
- PDB
- 5DOQ
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Geobacillus sp. PA-3; Geobacillus thermodenitrificans (strain NG80-2)
- Molecule
- Bd-type quinol oxidase subunit I; Bd-type quinol oxidase subunit II; Putative membrane…
- UniProt
- A4IKP6, A4IKP7, A0A0Q0UXS2
- Ligands
- HEB, HDD
- Pockets
- 9 · best druggability 0.90
Structure
x-ray diffraction · resolution 3.05 · 3 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bd-type quinol oxidase subunit I | protein | 432 | 71% helix, 5% strand | A4IKP6 |
| B | Bd-type quinol oxidase subunit II | protein | 330 | 76% helix, 0% strand | A4IKP7 |
| C | Putative membrane protein | protein | 30 | 87% helix, 0% strand | A0A0Q0UXS2 |
Ligands and binding sites
- HEB · Heme B/C · ligand · 2 copies · chains A, B
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.90 | 0.91 | 125 | HEB, HDD |
| 2 | 389 | 0.87 | 0.95 | 49 | empty |
| 3 | 361 | 0.68 | 0.81 | 27 | empty |
| 4 | 241 | 0.65 | 0.83 | 36 | empty |
| 5 | 67 | 0.54 | 0.85 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2583 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1141 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5DOQ · The structure of bd oxidase from geobacillus thermodenitrificans · the same entry in another collection · chain A against A, TM-score 1.00
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 A4IKP6
- Every structure of UniProt A4IKP7
- Every structure of UniProt A0A0Q0UXS2
- Elsewhere: RCSB PDB 5DOQ · PDBe 5DOQ · UniProt A4IKP6 · UniProt A4IKP7 · UniProt A0A0Q0UXS2
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