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Pseudomonas stutzeri nitrous oxide reductase, P65 crystal form

Analyse Pseudomonas stutzeri nitrous oxide reductase, P65 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SBQ
Type: protein
Length: 1,162 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrous-oxide reductase
EC: 1.7.99.6
UniProt: P19573
Ligands: CUA, CUK, K, CA, CL
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrous-oxide reductase (EC 1.7.99.6)	protein	581	11% helix, 41% strand	P19573

Ligands and binding sites

CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
CUK · [4Cu:2S] cluster · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
IMD · Imidazole · additive · chains A, B

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

Pockets

8 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	280	0.81	0.92	46	empty
2	187	0.46	0.75	28	empty
3	147	0.43	0.75	23	empty
4	111	0.39	0.75	25	empty
5	92	0.34	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 5824 Å² buried · 69 hydrogen bonds · protein-protein

Compared structures

3SBQ · Pseudomonas stutzeri nitrous oxide reductase, P65 crystal form · the same entry in another collection · chain A against A, TM-score 1.00
P19573 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (P19573) · 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 P19573
Elsewhere: RCSB PDB 3SBQ · PDBe 3SBQ · UniProt P19573

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