› 1x9d

X-ray diffraction
1.41Å resolution

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue

Released:
DOI: 10.2210/pdb1x9d/pdb
PDB entry 1x9d coloured by chain, front view.
PDB entry 1x9d coloured by chain, side view.
PDB entry 1x9d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.
Karaveg K, Siriwardena A, Tempel W, Liu ZJ, Glushka J, Wang BC, Moremen KW
J Biol Chem 280 16197-207 (2005)
PMID: 15713668

Function and Biology Details

Reaction catalysed: 
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193855 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase Chain: A
Molecule details ›
Chain: A
Length: 538 amino acids
Theoretical weight: 61.43 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9UKM7 (Residues: 172-699; Coverage: 76%)
Gene names: MAN1B1, UNQ747/PRO1477
Sequence domains: Glycosyl hydrolase family 47
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: Z5L, MAN
Ligand Z5L 1 x Z5L
Ligand MAN 1 x MAN
3 bound ligands:
Ligand CA 1 x CA
Ligand SO4 1 x SO4
Ligand BU1 1 x BU1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 50.687Å b: 53.878Å c: 56.234Å
α: 89.49° β: 63.6° γ: 62.61°
R-values:
R R work R free
0.146 0.144 0.162
Expression system: Komagataella pastoris

Quick links

Citations

13 review citations

In and out of the ER: protein folding, quality control, degradation, and related human diseases.
Hebert et al. (2007)
12 more

12 mentions without citation

N-linked glycan recognition and processing: the molecular basis of endoplasmic reticulum quality control.
Moremen et al. (2006)
11 more