MolNFT v1 · #17107 · protein

Family 1 B-glucosidase from thermotoga maritima

1OIN · Beta-glucosidase a: “Family 1 B-glucosidase from thermotoga maritima”. X-ray diffraction, 1 ligand (G2F), 4 pockets (best druggability 0.73). MolNFT v1 #17107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1OIN
Type: protein
Length: 885 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucosidase a
EC: 3.2.1.21
UniProt: Q08638
Ligands: G2F
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase a (EC 3.2.1.21)	protein	442	45% helix, 18% strand	Q08638
B	Beta-glucosidase a (EC 3.2.1.21)	protein	443	46% helix, 18% strand	Q08638

Ligands and binding sites

G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	650	0.73	0.79	53	G2F
2	527	0.71	0.80	52	G2F
3	94	0.33	0.73	21	empty
4	71	0.32	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 149 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1OIN · Family 1 b-glucosidase from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · a predicted model of the same protein · chain B 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 Q08638
Elsewhere: RCSB PDB 1OIN · PDBe 1OIN · UniProt Q08638

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