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Crystal structure of a GH1 beta-glucosidase from hamamotoa singularis

Analyse Crystal structure of a GH1 beta-glucosidase from hamamotoa singularis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M4E
Type: protein
Length: 542 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase-like enzyme
UniProt: Q564N5
Ligands: NAG, MAN
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-galactosidase-like enzyme	protein	542	45% helix, 11% strand	Q564N5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 53 copies · chains A

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

Pockets

2 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	539	0.68	0.78	58	EDO
2	93	0.34	0.74	26	EDO

Modifications

Observed in the structure: 7 glycan, 3 disulfide (N-glycosylation, disulfide, O-glycosylation).

Compared structures

6M4E · Crystal structure of a GH1 beta-glucosidase from Hamamotoa singularis · 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 Q564N5
Elsewhere: RCSB PDB 6M4E · PDBe 6M4E · UniProt Q564N5

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