MolNFT v1 · #12192 · protein

Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from bacillus stearothermophilus T-6, complexed with aldotetraouronic acid

1K9F: “Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from bacillus stearothermophilus T-6…”. X-ray diffraction, 2 ligands (GCV, XYP), 7 pockets (best druggability 0.52). MolNFT v1 #12192 on GenesisL1: 3D structure…

PDB: 1K9F
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: GCV, XYP
Pockets: 7 · best druggability 0.52

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

GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · chains A
XYP · beta-D-xylopyranose · sugar · 2 copies · chains A
GOL · Glycerol · additive · 12 copies · chains A

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

Pockets

7 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	111	0.52	0.82	20	XYP, GCV
2	164	0.49	0.77	24	empty
3	83	0.46	0.81	14	GOL
4	72	0.45	0.82	21	GOL
5	66	0.36	0.79	17	GOL

Compared structures

1K9F · Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from Bacillus… · 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
Elsewhere: RCSB PDB 1K9F · PDBe 1K9F

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