Research workbench
Structure of nitroreductase from E. cloacae bound with 2E-reduced flavin mononucleotide (FMN)
Analyse Structure of nitroreductase from E. cloacae bound with 2E-reduced flavin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KQD
- 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
- 1.6.6.-
- UniProt
- Q01234
- Ligands
- FMN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.6.6.-) | protein | 216 | 55% helix, 15% strand | Q01234 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.76 | 0.84 | 42 | FMN |
| 2 | 682 | 0.75 | 0.81 | 71 | FMN |
| 3 | 447 | 0.74 | 0.84 | 39 | FMN |
| 4 | 424 | 0.74 | 0.84 | 39 | FMN |
| 5 | 413 | 0.70 | 0.81 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3712 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3711 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1KQD · Structure of Nitroreductase from E. cloacae Bound with 2e-Reduced Flavin Mononucleotide… · 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 0.99
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 1KQD · PDBe 1KQD · UniProt Q01234
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