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The 1.5A crystal structure of alpha-D-glucuronidase from bacillus stearothermophilus T-1, complexed with 4-O-methyl-glucuronic acid and xylotriose

Analyse The 1.5A crystal structure of alpha-D-glucuronidase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L8N
Type: protein
Length: 671 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-D-glucuronidase
EC: 3.2.1.139
Ligands: GCW, XYP
Pockets: 6 · best druggability 0.58

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	671	39% helix, 13% strand	—

Ligands and binding sites

GCW · 4-O-methyl-beta-D-glucopyranuronic acid · ligand · chains A
XYP · beta-D-xylopyranose · sugar · 2 copies · chains A
GOL · Glycerol · additive · 14 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.58	0.85	24	XYP, GCW, GOL
2	51	0.54	0.89	27	empty
3	195	0.52	0.78	31	empty
4	75	0.44	0.81	15	GOL
5	86	0.42	0.78	13	GOL

Compared structures

1L8N · The 1.5A crystal structure of alpha-D-glucuronidase from Bacillus stearothermophilus T-1… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1L8N · PDBe 1L8N

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