› 6p4v

X-ray diffraction
1.65Å resolution

1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7

Released:
DOI: 10.2210/pdb6p4v/pdb
PDB entry 6p4v coloured by chain, front view.
PDB entry 6p4v coloured by chain, side view.
PDB entry 6p4v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase.
Tanaka Y, Kurasawa O, Yokota A, Klein MG, Ono K, Saito B, Matsumoto S, Okaniwa M, Ambrus-Aikelin G, Morishita D, Kitazawa S, Uchiyama N, Ogawa K, Kimura H, Imamura S
J Med Chem 63 3215-3226 (2020)
PMID: 32142284

Function and Biology Details

Reaction catalysed: 
(1a) spermidine + NAD(+) = dehydrospermidine + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155939 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyhypusine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 372 amino acids
Theoretical weight: 41.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49366 (Residues: 1-369; Coverage: 100%)
Gene names: DHPS, DS
Sequence domains: Deoxyhypusine synthase

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand GC7 2 x GC7
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P3221
Unit cell:
a: 104.466Å b: 104.466Å c: 159.49Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.162 0.161 0.175
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The eukaryotic initiation factor 5A (eIF5A1), the molecule, mechanisms and recent insights into the pathophysiological roles.
Tauc et al. (2021)
2 more

2 mentions without citation

New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase.
Tanaka et al. (2020)
1 more