› 4knw

X-ray diffraction
2.7Å resolution

The crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE

Released:
DOI: 10.2210/pdb4knw/pdb
PDB entry 4knw coloured by chain, front view.
PDB entry 4knw coloured by chain, side view.
PDB entry 4knw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: observation of extensive dynamics in an enzyme/inhibitor complex.
Kim SH, Constantine KL, Duke GJ, Goldfarb V, Hunt JT, Johnson S, Kish K, Klei HE, McDonnell PA, Metzler WJ, Mueller L, Poss MA, Fairchild CR, Bhide RS
Bioorg Med Chem Lett 23 4107-11 (2013)
PMID: 23747226

Function and Biology Details

Reaction catalysed: 
N-acylneuraminate 9-phosphate + H(2)O = N-acylneuraminate + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186176 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-acylneuraminate-9-phosphatase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 257 amino acids
Theoretical weight: 28.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8TBE9 (Residues: 2-248; Coverage: 100%)
Gene names: C20orf147, HDHD4, NANP
Sequence domains: haloacid dehalogenase-like hydrolase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand VO4 3 x VO4
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 46.777Å b: 102.56Å c: 186.665Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.254 0.296
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Designing sugar mimetics: non-natural pyranosides as innovative chemical tools.
Saliba et al. (2016)
1 other article