Research workbench

Nitric oxide bound to cu nitrite reductase

Analyse Nitric oxide bound to cu nitrite reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SNR
Type: protein
Length: 1,009 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Copper-containing nitrite reductase
EC: 1.7.2.1
UniProt: P38501
Ligands: CU1, CU, NO
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Copper-containing nitrite reductase (EC 1.7.2.1)	protein	336	12% helix, 43% strand	P38501
B	Copper-containing nitrite reductase (EC 1.7.2.1)	protein	337	12% helix, 43% strand	P38501

Ligands and binding sites

CU1 · Copper (I) ion · metal · 3 copies · chains A, B, C
CU · Copper (II) ion · metal · 3 copies · chains A, B, C
NO · Nitric oxide · ion · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 8 copies · chains A, B, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C

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

Pockets

15 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	277	0.85	0.96	27	TRS
2	499	0.81	0.88	59	ACT
3	65	0.73	0.97	17	empty
4	61	0.72	0.98	17	empty
5	55	0.70	0.97	19	ACT

Interfaces

3 interfaces between chains.

A–B · 2161 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 2107 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 2105 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

1SNR · Nitric oxide bound to Cu nitrite reductase · the same entry in another collection · chain A against A, TM-score 1.00
P38501 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P38501) · 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 P38501
Elsewhere: RCSB PDB 1SNR · PDBe 1SNR · UniProt P38501

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