› 6gpl

X-ray diffraction
1.76Å resolution

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man

Released:
DOI: 10.2210/pdb6gpl/pdb
PDB entry 6gpl coloured by chain, front view.
PDB entry 6gpl coloured by chain, side view.
PDB entry 6gpl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Pfeiffer M, Johansson C, Krojer T, Kavanagh KL, Oppermann U, Nidetzky B
ACS Catal 9 2962-2968 (2019)
PMID: 30984471

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: B, C, D, E
Molecule details ›
Chains: B, C, D, E
Length: 352 amino acids
Theoretical weight: 40.06 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 BCN 1 x BCN
Ligand F7E 4 x F7E
Ligand EDO 9 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 89.26Å b: 122.77Å c: 139.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.19
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential.
Vogel et al. (2022)
7 other articles

2 mentions without citation

A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Pfeiffer et al. (2019)
1 more