MolNFT v1 · #124148 · protein

Structure of a GH3 B-glucosidase from cow rumen metagenome in complex with galactose

5K6O: “Structure of a GH3 B-glucosidase from cow rumen metagenome in complex with galactose”. X-ray diffraction, 2 ligands (GAL, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #124148 on GenesisL1: 3D structure, binding sites and…

PDB: 5K6O
Type: protein
Length: 795 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-glucosidase
EC: 3.2.1.21
Ligands: GAL, SO4
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B-glucosidase (EC 3.2.1.21)	protein	795	30% helix, 23% strand	—

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 8 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.62	0.80	46	empty
2	122	0.55	0.83	17	empty
3	276	0.53	0.75	33	SO4
4	82	0.52	0.84	18	GAL
5	177	0.44	0.74	30	empty

Compared structures

5K6O · Structure of a GH3 b-glucosidase from cow rumen metagenome in complex with galactose · 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
Elsewhere: RCSB PDB 5K6O · PDBe 5K6O

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