Research workbench
The structure of bd oxidase from geobacillus thermodenitrificans
Analyse The structure of bd oxidase from geobacillus thermodenitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IR6
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bd-type quinol oxidase subunit I; Bd-type quinol oxidase subunit II; Putative membrane…
- UniProt
- Q9Z9N1, Q9Z9N0, A0A0Q0UXS2
- Ligands
- HEB, HDD
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 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 | Q9Z9N1 |
| B | Bd-type quinol oxidase subunit II | protein | 330 | 76% helix, 0% strand | Q9Z9N0 |
| 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.89 | 0.90 | 94 | HEB, HDD |
| 2 | 376 | 0.87 | 0.95 | 49 | empty |
| 3 | 279 | 0.80 | 0.91 | 44 | HEB |
| 4 | 354 | 0.68 | 0.81 | 27 | empty |
| 5 | 242 | 0.64 | 0.82 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2595 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1137 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5IR6 · 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 Q9Z9N1
- Every structure of UniProt Q9Z9N0
- Every structure of UniProt A0A0Q0UXS2
- Elsewhere: RCSB PDB 5IR6 · PDBe 5IR6 · UniProt Q9Z9N1 · UniProt Q9Z9N0 · UniProt A0A0Q0UXS2
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