Research workbench

NADH binding site and catalysis of NADH peroxidase

Analyse NADH binding site and catalysis of NADH peroxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NPX
Type: protein
Length: 447 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH peroxidase
EC: 1.11.1.1
UniProt: P37062
Ligands: FAD, NAD
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NADH peroxidase (EC 1.11.1.1)	protein	447	28% helix, 30% strand	P37062

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.78	0.80	92	FAD, NAD
2	72	0.44	0.81	23	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

2NPX · NADH binding site and catalysis of NADH peroxidase · the same entry in another collection · chain A against A, TM-score 1.00
P37062 · AlphaFold monomer V2.0 prediction for NADH peroxidase (P37062) · 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 P37062
Elsewhere: RCSB PDB 2NPX · PDBe 2NPX · UniProt P37062

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.