3DGR Transferase date Jun 15, 2008
title Crystal Structure Of Human Nampt Complexed With Adp Analogue
authors M.Ho, E.S.Burgos, S.C.Almo, V.L.Schramm
compound source
Molecule: Nicotinamide Phosphoribosyltransferase
Chain: A, B
Synonym: Namprtase, Nampt, Pre-B Cell-Enhancing Factor, Pre Colony-Enhancing Factor 1, Visfatin;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Nampt, Pbef, Pbef1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdest
symmetry Space Group: P 1 21 1
R_factor 0.180 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
61.290 107.229 82.661 90.00 96.41 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand A12 enzyme Transferase E.C. BRENDA
A, B

Primary referenceA 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. 2009 Aug 4. PMID:19666527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk]
  • Biological Unit Coordinates (3dgr.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 3DGR
  • CSU: Contacts of Structural Units for 3DGR
  • Structure Factors (912 Kb)
  • Retrieve 3DGR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DGR from S2C, [Save to disk]
  • Re-refined 3dgr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DGR in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3DGR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3DGR, from MSDmotif at EBI
  • Fold representative 3dgr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dgr_A] [3dgr_B] [3dgr]
  • SWISS-PROT database: [P43490]
  • Domain organization of [NAMPT_HUMAN] by SWISSPFAM
  • Other resources with information on 3DGR
  • Community annotation for 3DGR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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