MolNFT v1 · #110215 · protein

Crystal structure of the mutant D365A of pedobacter saltans GH31 alpha-galactosidase complexed with P-nitrophenyl-alpha- galactopyranoside

4XPS · Alpha-glucosidase: “Crystal structure of the mutant D365A of pedobacter saltans GH31 alpha-galactosidase complexed with…”. X-ray diffraction, 2 ligands (NPO, GLA), 8 pockets (best druggability 0.72). MolNFT v1 #110215 on GenesisL1…

PDB: 4XPS
Type: protein
Length: 665 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-glucosidase
EC: 3.2.1.22
Ligands: NPO, GLA
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-glucosidase (EC 3.2.1.22)	protein	665	23% helix, 25% strand	—

Ligands and binding sites

NPO · P-nitrophenol · ligand · chains A
GLA · alpha-D-galactopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

8 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	52	0.72	0.99	17	empty
2	221	0.55	0.78	26	empty
3	168	0.51	0.78	31	EDO
4	109	0.43	0.77	20	EDO
5	62	0.40	0.80	14	empty

Compared structures

4XPS · Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase… · 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 4XPS · PDBe 4XPS

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