MolNFT v1 · #15751 · protein

Nitroreductase from enterobacter cloacae

1NEC · Protein (nitroreductase): “Nitroreductase from enterobacter cloacae”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.76). MolNFT v1 #15751 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NEC
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (nitroreductase)
UniProt: Q01234
Ligands: FMN
Pockets: 7 · 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	Protein (nitroreductase)	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

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	737	0.76	0.81	65	FMN
2	640	0.76	0.82	63	FMN
3	673	0.76	0.81	58	FMN
4	458	0.75	0.84	46	FMN
5	839	0.71	0.77	65	empty

Interfaces

4 interfaces between chains.

C–D · 3714 Å² buried · 59 hydrogen bonds · protein-protein
A–B · 3646 Å² buried · 55 hydrogen bonds · protein-protein
A–D · 107 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 98 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1NEC · Nitroreductase from enterobacter cloacae · 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 1NEC · PDBe 1NEC · UniProt Q01234

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