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Spaga D472N structure in complex with melibiose

Analyse Spaga D472N structure in complex with melibiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PHW
Type: protein
Length: 721 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-galactosidase
EC: 3.2.1.22
UniProt: A0A0H2URQ6
Ligands: GLC, GLA
Pockets: 6 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-galactosidase (EC 3.2.1.22)	protein	721	21% helix, 33% strand	A0A0H2URQ6

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains A
GLA · alpha-D-galactopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains A
TLA · L(+)-tartaric acid · additive · 2 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.49	0.85	19	GLC, GLA
2	107	0.42	0.77	23	EDO
3	139	0.41	0.74	29	empty
4	64	0.38	0.79	16	EDO
5	65	0.32	0.75	13	empty

Compared structures

6PHW · SpAga D472N structure in complex with melibiose · 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 A0A0H2URQ6
Elsewhere: RCSB PDB 6PHW · PDBe 6PHW · UniProt A0A0H2URQ6

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