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Nitrite bound copper containing nitrite reductase

Analyse Nitrite bound copper containing nitrite reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SJM
Type: protein
Length: 1,007 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: CU, NO2
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Copper-containing nitrite reductase (EC 1.7.2.1)	protein	335	12% helix, 42% strand	P38501
B, C	Copper-containing nitrite reductase (EC 1.7.2.1)	protein	336	12% helix, 42% strand	P38501

Ligands and binding sites

CU · Copper (II) ion · metal · 6 copies · chains A, B, C
NO2 · Nitrite ion · ion · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 5 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

13 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	284	0.84	0.96	27	TRS
2	523	0.80	0.87	61	ACT
3	67	0.73	0.98	17	empty
4	63	0.73	0.98	18	empty
5	62	0.72	0.98	20	empty

Interfaces

3 interfaces between chains.

B–C · 2106 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 2102 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 2086 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

1SJM · Nitrite bound copper containing 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 1SJM · PDBe 1SJM · UniProt P38501

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