› 6rrw

X-ray diffraction
2.15Å resolution

GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol

Released:
DOI: 10.2210/pdb6rrw/pdb
PDB entry 6rrw coloured by chain, front view.
PDB entry 6rrw coloured by chain, side view.
PDB entry 6rrw coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Manno-epi-cyclophellitols Enable Activity-Based Protein Profiling of Human α-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
Armstrong Z, Kuo CL, Lahav D, Liu B, Johnson R, Beenakker TJM, de Boer C, Wong CS, van Rijssel ER, Debets MF, Florea BI, Hissink C, Boot RG, Geurink PP, Ovaa H, van der Stelt M, van der Marel GM, Codée JDC, Aerts JMFG, Wu L, Overkleeft HS, Davies GJ
J Am Chem Soc 142 13021-13029 (2020)
PMID: 32605368

Function and Biology Details

Reaction catalysed: 
Man(5)GlcNAc(3)-[protein] + 2 H(2)O = Man(3)GlcNAc(3)-[protein] + 2 alpha-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173193 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-mannosidase 2 Chain: A
Molecule details ›
Chain: A
Length: 1033 amino acids
Theoretical weight: 118.21 KDa
Source organism: Drosophila melanogaster
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q24451 (Residues: 76-1108; Coverage: 93%)
Gene names: CG18802, GmII, alpha-Man-IIa
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand KG5 1 x KG5
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 89.171Å b: 91.671Å c: 132.316Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.2 0.265
Expression system: Trichoplusia ni

Quick links

Citations

3 review citations

Synthesis, Processing, and Function of N-Glycans in N-Glycoproteins.
Bieberich E. (2023)
2 more