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Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form

Analyse Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SBP
Type: protein
Length: 4,659 residues
Chains: 8
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, CA, K, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, H	Nitrous-oxide reductase (EC 1.7.99.6)	protein	581	10% helix, 42% strand	P19573
D	Nitrous-oxide reductase (EC 1.7.99.6)	protein	588	10% helix, 41% strand	P19573
G	Nitrous-oxide reductase (EC 1.7.99.6)	protein	585	10% helix, 42% strand	P19573

Ligands and binding sites

CUA · Dinuclear copper ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CUK · [4Cu:2S] cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
IMD · Imidazole · additive · 6 copies · chains C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.82	0.93	45	empty
2	271	0.81	0.92	46	empty
3	274	0.80	0.92	45	empty
4	455	0.77	0.86	63	empty
5	1020	0.71	0.75	90	empty

Interfaces

12 interfaces between chains.

A–B · 5901 Å² buried · 68 hydrogen bonds · protein-protein
G–H · 5893 Å² buried · 75 hydrogen bonds · protein-protein
C–D · 5853 Å² buried · 67 hydrogen bonds · protein-protein
E–F · 5803 Å² buried · 71 hydrogen bonds · protein-protein
D–E · 474 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3SBP · Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form · the same entry in another collection · chain H against H, 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 3SBP · PDBe 3SBP · UniProt P19573

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