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Structure of a GH3 B-glicosidase from cow rumen metagenome in complexed with xylose

Analyse Structure of a GH3 B-glicosidase from cow rumen metagenome in complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K6N
Type: protein
Length: 792 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-glucosidase
Ligands: XYP, SO4
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B-glucosidase	protein	792	30% helix, 24% strand	—

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 6 copies · chains A
GOL · Glycerol · additive · 5 copies · chains A

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

Pockets

6 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	278	0.63	0.81	47	GOL
2	137	0.56	0.82	23	empty
3	222	0.47	0.74	30	empty
4	154	0.41	0.74	25	empty
5	57	0.41	0.81	17	XYP

Compared structures

5K6N · Structure of a GH3 b-glicosidase from cow rumen metagenome in complexed with xylose · 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 5K6N · PDBe 5K6N

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