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Crystal structure of beta-glucuronidase from acidobacterium capsulatum in complex with D-glucuronic acid

Analyse Crystal structure of beta-glucuronidase from acidobacterium capsulatum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VNZ
Type: protein
Length: 466 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucuronidase
EC: 3.2.1.31
UniProt: C1F2K5
Ligands: BDP, PO4
Pockets: 4 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucuronidase (EC 3.2.1.31)	protein	466	30% helix, 30% strand	C1F2K5

Ligands and binding sites

BDP · beta-D-glucopyranuronic acid · sugar · chains A
PO4 · Phosphate ion · ion · chains A
GOL · Glycerol · additive · chains A

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

Pockets

4 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	218	0.62	0.82	29	BDP
2	147	0.46	0.76	29	empty
3	74	0.38	0.78	17	empty
4	63	0.29	0.74	20	empty

Compared structures

3VNZ · Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex 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 C1F2K5
Elsewhere: RCSB PDB 3VNZ · PDBe 3VNZ · UniProt C1F2K5

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