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The crystal structure of bacteroides fragilis beta-glucuronidase in complex with uronic isofagomine

Analyse The crystal structure of bacteroides fragilis beta-glucuronidase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z1A
Type: protein
Length: 655 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative beta-galactosidase
UniProt: Q5LIC7
Ligands: SJ5
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative beta-galactosidase	protein	655	16% helix, 39% strand	Q5LIC7

Ligands and binding sites

SJ5 · (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid · ligand · 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	368	0.65	0.79	41	empty
2	159	0.56	0.81	28	SJ5
3	125	0.48	0.79	22	empty
4	148	0.45	0.76	23	empty
5	61	0.42	0.82	17	empty

Compared structures

5Z1A · The crystal structure of Bacteroides fragilis beta-glucuronidase in complex with uronic… · 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 Q5LIC7
Elsewhere: RCSB PDB 5Z1A · PDBe 5Z1A · UniProt Q5LIC7

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