› 3dkl

X-ray diffraction
1.89Å resolution

Crystal structure of phosphorylated mimic form of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate

Released:
DOI: 10.2210/pdb3dkl/pdb
PDB entry 3dkl coloured by chain, front view.
PDB entry 3dkl coloured by chain, side view.
PDB entry 3dkl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.
Burgos ES, Ho MC, Almo SC, Schramm VL
Proc Natl Acad Sci U S A 106 13748-53 (2009)
PMID: 19666527

Function and Biology Details

Reaction catalysed: 
Nicotinamide D-ribonucleotide + diphosphate = nicotinamide + 5-phospho-alpha-D-ribose 1-diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155082 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nicotinamide phosphoribosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 484 amino acids
Theoretical weight: 54.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P43490 (Residues: 1-484; Coverage: 99%)
Gene names: NAMPT, PBEF, PBEF1
Sequence domains:
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand MG 4 x MG
Ligand UNU 2 x UNU
Ligand BEF 2 x BEF
Ligand PRP 2 x PRP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 61.127Å b: 106.589Å c: 83.24Å
α: 90° β: 96.78° γ: 90°
R-values:
R R work R free
0.179 0.177 0.214
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Nicotinamide phosphoribosyltransferase in malignancy: a review.
Shackelford et al. (2013)
11 more

4 mentions without citation

Structure-function of the G protein-coupled receptor superfamily.
Katritch et al. (2013)
3 more