Research workbench
Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide
Analyse Structure of nitroreductase from E. cloacae complexed with nicotinic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J8D
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- EC
- 1.-.-.-
- UniProt
- Q01234
- Ligands
- FMN, DND
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 216 | 56% helix, 15% strand | Q01234 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- DND · Nicotinic acid adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.75 | 0.82 | 47 | FMN, DND |
| 2 | 622 | 0.75 | 0.81 | 53 | DND, FMN |
| 3 | 582 | 0.74 | 0.81 | 43 | DND, FMN |
| 4 | 599 | 0.73 | 0.81 | 53 | FMN, DND |
| 5 | 229 | 0.56 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- C–D · 3611 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3524 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 5J8D · Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01234 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NAD(P)H nitroreductase (Q01234) · a predicted model of the same protein · 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 Q01234
- Elsewhere: RCSB PDB 5J8D · PDBe 5J8D · UniProt Q01234
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