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The 1.7 a crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus T-1

Analyse The 1.7 a crystal structure of alpha-D-glucuronidase, a family-67 glycoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K9D
Type: protein
Length: 670 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-D-glucuronidase
EC: 3.2.1.139
UniProt: Q8VVD2
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-D-glucuronidase (EC 3.2.1.139)	protein	670	39% helix, 13% strand	Q8VVD2

Ligands and binding sites

GOL · Glycerol · additive · 13 copies · chains A

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

Pockets

5 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	113	0.53	0.82	21	GOL
2	164	0.49	0.77	24	empty
3	68	0.43	0.81	15	GOL
4	91	0.41	0.78	16	GOL
5	58	0.36	0.79	15	empty

Compared structures

1K9D · The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase… · 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 Q8VVD2
Elsewhere: RCSB PDB 1K9D · PDBe 1K9D · UniProt Q8VVD2

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