MolNFT v1 · #8004 · protein

B-glucosidase from streptomyces sp

1GNX · Beta-glucosidase: “B-glucosidase from streptomyces sp”. X-ray diffraction, 3 ligands (GLC, FRU, SO4), 6 pockets (best druggability 0.71). MolNFT v1 #8004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1GNX
Type: protein
Length: 894 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucosidase
EC: 3.2.1.21
UniProt: Q59976
Ligands: GLC, FRU, SO4
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase (EC 3.2.1.21)	protein	447	43% helix, 16% strand	Q59976
B	Beta-glucosidase (EC 3.2.1.21)	protein	447	43% helix, 16% strand	Q59976

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains A
FRU · beta-D-fructofuranose · sugar · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

6 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	448	0.71	0.81	38	empty
2	430	0.70	0.81	39	empty
3	56	0.68	0.97	21	empty
4	65	0.43	0.81	21	empty
5	62	0.41	0.80	16	empty

Interfaces

1 interface between chains.

A–B · 1050 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1GNX · b-glucosidase from Streptomyces sp · the same entry in another collection · 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 Q59976
Elsewhere: RCSB PDB 1GNX · PDBe 1GNX · UniProt Q59976

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