MolNFT v1 · #154066 · protein

B-glucuronidase from ruminococcus gnavus in complex with D-glucuronic acid

6JZ5 · Beta-glucuronidase: “B-glucuronidase from ruminococcus gnavus in complex with D-glucuronic acid”. X-ray diffraction, 1 ligand (BDP), 12 pockets (best druggability 0.86). MolNFT v1 #154066 on GenesisL1: 3D structure, binding sites…

PDB: 6JZ5
Type: protein
Length: 1,148 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucuronidase
UniProt: Q6W7J7
Ligands: BDP
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucuronidase	protein	572	22% helix, 35% strand	Q6W7J7
B	Beta-glucuronidase	protein	576	21% helix, 35% strand	Q6W7J7

Ligands and binding sites

BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.86	0.87	87	empty
2	680	0.70	0.78	80	empty
3	66	0.59	0.90	22	empty
4	70	0.55	0.87	23	empty
5	263	0.55	0.77	34	BDP

Interfaces

1 interface between chains.

A–B · 1621 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6JZ5 · b-glucuronidase from Ruminococcus gnavus in complex with D-glucuronic acid · 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 Q6W7J7
Elsewhere: RCSB PDB 6JZ5 · PDBe 6JZ5 · UniProt Q6W7J7

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