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Crystal structure of nagz from pseudomonas aeruginosa

Analyse Crystal structure of nagz from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G1M
Type: protein
Length: 666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-hexosaminidase
EC: 3.2.1.52
UniProt: Q9HZK0
Ligands: CL
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-hexosaminidase (EC 3.2.1.52)	protein	333	41% helix, 14% strand	Q9HZK0

Ligands and binding sites

CL · Chloride ion · ion · chains A
ACT · Acetate ion · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	967	0.75	0.78	73	empty
2	413	0.65	0.78	38	empty
3	197	0.51	0.77	22	empty
4	164	0.47	0.76	28	empty
5	90	0.32	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 452 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5G1M · Crystal structure of NagZ from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
Q9HZK0 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q9HZK0) · a predicted model of the same protein · chain A against A, TM-score 0.93

Analyse

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Every structure of UniProt Q9HZK0
Elsewhere: RCSB PDB 5G1M · PDBe 5G1M · UniProt Q9HZK0

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