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Structure of the GH99 endo-alpha-mannosidase from bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose

Analyse Structure of the GH99 endo-alpha-mannosidase from bacteroides xylanisolvens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AD5
Type: protein
Length: 348 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosyl hydrolase family 71
EC: 3.2.1.130
UniProt: D6D1V7
Ligands: DMJ, MAN, GLC
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosyl hydrolase family 71 (EC 3.2.1.130)	protein	348	35% helix, 16% strand	D6D1V7

Ligands and binding sites

DMJ · 1-deoxymannojirimycin · ligand · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
GLC · alpha-D-glucopyranose · sugar · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.47	0.78	26	MAN, GLC, DMJ
2	92	0.43	0.79	13	empty

Compared structures

4AD5 · Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex… · 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 D6D1V7
Elsewhere: RCSB PDB 4AD5 · PDBe 4AD5 · UniProt D6D1V7

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