3KVV Transferase date Nov 30, 2009
title Trapping Of An Oxocarbenium Ion Intermediate In Up Crystals
authors D.Paul, S.O'Leary, K.Rajashankar, W.Bu, A.Toms, E.Settembre, J.San T.P.Begley, S.E.Ealick
compound source
Molecule: Uridine Phosphorylase
Chain: A, B, C, D, E, F
Synonym: Urdpase, Upase
Ec: 2.4.2.3
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
Gene: Udp
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Xf1
symmetry Space Group: P 32
R_factor 0.173 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.864 92.864 145.016 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand R2B, SO4, URF enzyme Transferase E.C.2.4.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceGlycal formation in crystals of uridine phosphorylase., Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE, Biochemistry. 2010 Apr 27;49(16):3499-509. PMID:20364833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (3kvv.pdb1.gz) 231 Kb
  • LPC: Ligand-Protein Contacts for 3KVV
  • CSU: Contacts of Structural Units for 3KVV
  • Structure Factors (1738 Kb)
  • Retrieve 3KVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KVV from S2C, [Save to disk]
  • Re-refined 3kvv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KVV 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 3KVV
  • 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
  • 3D motif for 3KVV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kvv_F] [3kvv_A] [3kvv_D] [3kvv_B] [3kvv_C] [3kvv] [3kvv_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KVV
  • Community annotation for 3KVV 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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