MolNFT v1 · #1021 · protein

Cytochrome CD1 nitrite reductase with substrate and product bound

1AOQ: “Cytochrome CD1 nitrite reductase with substrate and product bound”. X-ray diffraction, 4 ligands (HEM, DHE, 2NO), 10 pockets (best druggability 0.87). MolNFT v1 #1021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1AOQ
Type: protein
Length: 1,110 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrite reductase
UniProt: P72181
Ligands: HEM, DHE, 2NO, NO
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrite reductase	protein	551	15% helix, 36% strand	P72181
B	Nitrite reductase	protein	559	17% helix, 36% strand	P72181

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
DHE · Heme D · ligand · 2 copies · chains A, B
2NO · Nitrogen dioxide · ligand · chains A
NO · Nitric oxide · ion · chains B

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.87	0.94	53	DHE, 2NO
2	795	0.86	0.89	97	HEM, DHE, NO
3	226	0.84	0.96	34	empty
4	1021	0.77	0.79	76	empty
5	234	0.65	0.83	42	HEM

Interfaces

1 interface between chains.

A–B · 1370 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (heme attachment).

Compared structures

1AOQ · Cytochrome CD1 nitrite reductase with substrate and product bound · the same entry in another collection · chain A against A, TM-score 1.00
P72181 · AlphaFold monomer V2.0 prediction for nitrite reductase (P72181) · 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 P72181
Elsewhere: RCSB PDB 1AOQ · PDBe 1AOQ · UniProt P72181

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