› 5kk7

X-ray diffraction
1.73Å resolution

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase T688A mutant and Thio-disaccharide substrate analog complex

Released:
DOI: 10.2210/pdb5kk7/pdb
PDB entry 5kk7 coloured by chain, front view.
PDB entry 5kk7 coloured by chain, side view.
PDB entry 5kk7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
Xiang Y, Karaveg K, Moremen KW
Proc Natl Acad Sci U S A 113 E7890-E7899 (2016)
PMID: 27856750

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 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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 455 amino acids
Theoretical weight: 52.27 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9UKM7 (Residues: 245-699; Coverage: 65%)
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 2 x Z5L
Ligand MAN 2 x MAN
5 bound ligands:
Ligand CA 2 x CA
Ligand SO4 3 x SO4
Ligand 1PS 2 x 1PS
Ligand BU1 4 x BU1
Ligand ACT 5 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P1
Unit cell:
a: 53.887Å b: 56.302Å c: 89.555Å
α: 105.68° β: 94.15° γ: 114.25°
R-values:
R R work R free
0.177 0.176 0.209
Expression system: Komagataella pastoris

Quick links

Citations

3 review citations

Exploitation of glycosylation in enveloped virus pathobiology.
Watanabe et al. (2019)
2 more

2 mentions without citation

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
Xiang et al. (2016)
1 more