Research workbench
The crystal structure of nitroreductase a from vibrio parahaemolyticus rimd 2210633
Analyse The crystal structure of nitroreductase a from vibrio parahaemolyticus rimd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UU6
- Type
- protein
- Length
- 937 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-flavin oxidoreductase
- UniProt
- Q87FS7
- Ligands
- FMN, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-flavin oxidoreductase | protein | 233 | 49% helix, 15% strand | Q87FS7 |
| B | NADPH-flavin oxidoreductase | protein | 233 | 49% helix, 14% strand | Q87FS7 |
| C | NADPH-flavin oxidoreductase | protein | 236 | 48% helix, 14% strand | Q87FS7 |
| D | NADPH-flavin oxidoreductase | protein | 235 | 49% helix, 14% strand | Q87FS7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.75 | 0.78 | 110 | FMN, CL |
| 2 | 238 | 0.63 | 0.82 | 38 | FMN |
| 3 | 250 | 0.61 | 0.80 | 40 | FMN, CL |
Interfaces
3 interfaces between chains.
- C–D · 4735 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4647 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 5UU6 · The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633 · 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 Q87FS7
- Elsewhere: RCSB PDB 5UU6 · PDBe 5UU6 · UniProt Q87FS7
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