2E5D Transferase date Dec 20, 2006
title Crystal Structure Of Human Nmprtase Complexed With Nicotinam
authors R.Takahashi, S.Nakamura, Y.Kobayashi, T.Ohkubo
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_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p1
symmetry Space Group: P 1 21 1
R_factor 0.179 R_Free 0.209
length a length b length c angle alpha angle beta angle gamma
60.332 106.227 82.475 90.00 96.27 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NCA enzyme Transferase E.C. BRENDA
A, B

Primary referenceStructure and reaction mechanism of human nicotinamide phosphoribosyltransferase., Takahashi R, Nakamura S, Nakazawa T, Minoura K, Yoshida T, Nishi Y, Kobayashi Y, Ohkubo T, J Biochem. 2010 Jan;147(1):95-107. Epub 2009 Oct 9. PMID:19819904
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (2e5d.pdb1.gz) 164 Kb
  • LPC: Ligand-Protein Contacts for 2E5D
  • CSU: Contacts of Structural Units for 2E5D
  • Likely Quarternary Molecular Structure file(s) for 2E5D
  • Structure Factors (1040 Kb)
  • Retrieve 2E5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E5D from S2C, [Save to disk]
  • Re-refined 2e5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E5D 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 2E5D
  • 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 2E5D, from MSDmotif at EBI
  • Fold representative 2e5d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e5d_A] [2e5d] [2e5d_B]
  • SWISS-PROT database: [P43490]
  • Domain organization of [NAMPT_HUMAN] by SWISSPFAM
  • Other resources with information on 2E5D
  • Community annotation for 2E5D 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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