Research workbench
The crystal structure of azoreductase from yersinia pestis CO92 in its apo form
Analyse The crystal structure of azoreductase from yersinia pestis CO92 in its apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRO
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent NADH-azoreductase
- EC
- 1.7.-.-
- UniProt
- Q8ZE60
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 184 | 40% helix, 21% strand | Q8ZE60 |
| B | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 182 | 42% helix, 23% strand | Q8ZE60 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.54 | 0.76 | 19 | GOL |
| 2 | 69 | 0.42 | 0.81 | 20 | empty |
| 3 | 114 | 0.41 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1213 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- Q8ZE60 · AlphaFold monomer V2.0 prediction for FMN-dependent NADH:QUINONE oxidoreductase (Q8ZE60) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8ZE60
- Elsewhere: RCSB PDB 5JRO · PDBe 5JRO · UniProt Q8ZE60
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