MolNFT v1 · #114682 · protein

Crystal structure of thermoanaerobacterium xylanolyticum GH116 beta- glucosidase with deoxynojirimycin

5BX3 · Beta-glucosidase: “Crystal structure of thermoanaerobacterium xylanolyticum GH116 beta- glucosidase with deoxynojirimycin”. X-ray diffraction, 2 ligands (NOJ, CA), 5 pockets (best druggability 0.52). MolNFT v1 #114682 on GenesisL1…

PDB: 5BX3
Type: protein
Length: 769 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucosidase
EC: 3.2.1.21
UniProt: F6BL85
Ligands: NOJ, CA
Pockets: 5 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase (EC 3.2.1.21)	protein	769	31% helix, 23% strand	F6BL85

Ligands and binding sites

NOJ · 1-deoxynojirimycin · ligand · chains A
CA · Calcium ion · metal · chains A
GOL · Glycerol · additive · 15 copies · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.52	0.78	30	NOJ, GOL
2	129	0.43	0.76	20	empty
3	76	0.38	0.77	15	GOL
4	57	0.35	0.79	18	GOL
5	58	0.30	0.75	13	GOL

Compared structures

5BX3 · Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with… · 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 F6BL85
Elsewhere: RCSB PDB 5BX3 · PDBe 5BX3 · UniProt F6BL85

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