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Crystal structure of pedobacter saltans GH31 alpha-galactosidase complexed with L-fucose

Analyse Crystal structure of pedobacter saltans GH31 alpha-galactosidase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XPQ
Type: protein
Length: 670 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-glucosidase
EC: 3.2.1.22
Ligands: FUL
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-glucosidase (EC 3.2.1.22)	protein	670	23% helix, 27% strand	—

Ligands and binding sites

FUL · beta-L-fucopyranose · sugar · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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	221	0.55	0.78	26	empty
2	168	0.45	0.75	34	EDO
3	65	0.42	0.81	18	EDO
4	55	0.39	0.81	15	empty
5	90	0.38	0.76	23	empty

Compared structures

4XPQ · Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with L-fucose · 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 4XPQ · PDBe 4XPQ

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