4YUB Ligase date Mar 18, 2015
title Crystal Structure Of Human Nicotinic Acid Phosphoribosyltran
authors S.Garavaglia, M.Rizzi, A.S.Marletta
compound source
Molecule: Nicotinate Phosphoribosyltransferase
Chain: A, B
Synonym: Naprtase,Fha-Hit-Interacting Protein,Nicotinate Phosphoribosyltransferase Domain-Containing Protein 1;
Ec: 6.3.4.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Naprt, Fhip, Naprt1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.018 101.091 125.144 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand
enzyme Ligase E.C.6.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of human nicotinic acid phosphoribosyltransferase., Marletta AS, Massarotti A, Orsomando G, Magni G, Rizzi M, Garavaglia S, FEBS Open Bio. 2015 May 7;5:419-28. doi: 10.1016/j.fob.2015.05.002. eCollection, 2015. PMID:26042198
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (162 Kb) [Save to disk]
  • Biological Unit Coordinates (4yub.pdb1.gz) 155 Kb
  • CSU: Contacts of Structural Units for 4YUB
  • Structure Factors (466 Kb)
  • Retrieve 4YUB in mmCIF format [Save to disk]
  • Re-refined 4yub structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YUB 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 4YUB
  • 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 4YUB, from MSDmotif at EBI
  • Fold representative 4yub from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yub_A] [4yub_B] [4yub]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YUB
  • Community annotation for 4YUB at PDBWiki (http://pdbwiki.org)

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