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Beta-glucosidase from thermotoga maritima in complex with N- octyl-5-deoxy-6-oxa-N-(THIO)CARBAMOYLCALYSTEGINE

Analyse Beta-glucosidase from thermotoga maritima in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VRJ
Type: protein
Length: 881 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: NCW, CA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase a (EC 3.2.1.21)	protein	438	45% helix, 19% strand	Q08638
B	Beta-glucosidase a (EC 3.2.1.21)	protein	443	45% helix, 19% strand	Q08638

Ligands and binding sites

NCW · (1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

3 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	595	0.72	0.80	52	NCW
2	462	0.71	0.80	42	NCW
3	78	0.36	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 73 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2VRJ · Beta-glucosidase from Thermotoga maritima in complex with N-octyl-5… · 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 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 Q08638
Elsewhere: RCSB PDB 2VRJ · PDBe 2VRJ · UniProt Q08638

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