MolNFT v1 · #84067 · protein
Crystal structure of escherichia COLI nitroreductase nfsb mutant T41L/N71S/F124W
3X21 · Oxygen-insensitive NAD(P)H nitroreductase: “Crystal structure of escherichia COLI nitroreductase nfsb mutant T41L/N71S/F124W”. X-ray diffraction, 1 ligand (FMN), 13 pockets (best druggability 0.88). MolNFT v1 #84067 on GenesisL1: 3D…
- PDB
- 3X21
- Type
- protein
- Length
- 2,170 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- EC
- 1.5.1.34
- UniProt
- P38489
- Ligands
- FMN
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.5.1.34) | protein | 217 | 51% helix, 15% strand | P38489 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.88 | 0.89 | 101 | FMN |
| 2 | 767 | 0.86 | 0.89 | 96 | FMN |
| 3 | 867 | 0.82 | 0.84 | 87 | FMN |
| 4 | 529 | 0.79 | 0.86 | 61 | empty |
| 5 | 695 | 0.78 | 0.83 | 65 | FMN |
Interfaces
19 interfaces between chains.
- I–J · 3703 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3654 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 3654 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3637 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3563 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 3X21 · Crystal structure of Escherichia coli nitroreductase NfsB mutant T41L/N71S/F124W · the same entry in another collection · chain J against J, TM-score 1.00
- P38489 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NAD(P)H nitroreductase (P38489) · 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 P38489
- Elsewhere: RCSB PDB 3X21 · PDBe 3X21 · UniProt P38489
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