Research workbench

Glycoside hydrolase B with product

Analyse Glycoside hydrolase B with product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GSM
Type: protein
Length: 1,572 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exo-beta-D-glucosaminidase
UniProt: Q76HN4
Ligands: GCS
Pockets: 16 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Exo-beta-D-glucosaminidase	protein	786	31% helix, 27% strand	Q76HN4

Ligands and binding sites

GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B
PPI · Propanoic acid · additive · 9 copies · chains A, B
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

16 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	877	0.73	0.77	73	GCS, PEG, PPI
2	855	0.73	0.78	77	GCS, PEG, PPI
3	428	0.67	0.80	64	empty
4	135	0.56	0.83	27	PPI
5	253	0.56	0.77	35	empty

Interfaces

1 interface between chains.

A–B · 2846 Å² buried · 68 hydrogen bonds · protein-protein

Compared structures

5GSM · Glycoside hydrolase B with product · the same entry in another collection · chain A against A, TM-score 1.00
Q76HN4 · AlphaFold monomer V2.0 prediction for exo-beta-D-glucosaminidase (Q76HN4) · 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 Q76HN4
Elsewhere: RCSB PDB 5GSM · PDBe 5GSM · UniProt Q76HN4

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