› 5in5

X-ray diffraction
1.9Å resolution

Crystal Structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor GDP-Fucose

Released:
DOI: 10.2210/pdb5in5/pdb
PDB entry 5in5 coloured by chain, front view.
PDB entry 5in5 coloured by chain, side view.
PDB entry 5in5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.
Allen JG, Mujacic M, Frohn MJ, Pickrell AJ, Kodama P, Bagal D, San Miguel T, Sickmier EA, Osgood S, Swietlow A, Li V, Jordan JB, Kim KW, Rousseau AC, Kim YJ, Caille S, Achmatowicz M, Thiel O, Fotsch CH, Reddy P, McCarter JD
ACS Chem Biol 11 2734-2743 (2016)
PMID: 27434622

Function and Biology Details

Reaction catalysed: 
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130014 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose 4,6 dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 364 amino acids
Theoretical weight: 41.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60547 (Residues: 23-372; Coverage: 94%)
Gene name: GMDS
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 4 x NAP
3 bound ligands:
Ligand GDP 4 x GDP
Ligand GFB 4 x GFB
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 63.137Å b: 140.164Å c: 86.028Å
α: 90° β: 106.32° γ: 90°
R-values:
R R work R free
0.152 0.149 0.198
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Glycoengineering of Antibodies for Modulating Functions.
Wang et al. (2019)
6 more

1 mention without citation

Structural and functional analysis of parameters governing tankyrase-1 interaction with telomeric repeat-binding factor 1 and GDP-mannose 4,6-dehydratase.
Eisemann et al. (2019)