5D3V Lipid Binding Protein date Aug 06, 2015
title Crystal Structure Of The P-Rex1 Ph Domain With Citrate Bound
authors J.N.Cash, J.J.G.Tesmer
compound source
Molecule: Phosphatidylinositol 3,4,5-Trisphosphate-Dependen Exchanger 1 Protein;
Chain: A, B
Fragment: Unp Residues 245-408
Synonym: Ptdins(3,4,5)-Dependent Rac Exchanger 1
Engineered: Yes
Other_details: Pleckstrin Homology Domain
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prex1, Kiaa1415
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmalc2h10t
symmetry Space Group: P 21 21 21
R_factor 0.172 R_Free 0.216
length a length b length c angle alpha angle beta angle gamma
54.080 72.424 82.526 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand FLC enzyme
Primary referenceStructural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3., Cash JN, Davis EM, Tesmer JJ, Structure. 2016 May 3;24(5):730-40. doi: 10.1016/j.str.2016.02.022. Epub 2016 Apr, 14. PMID:27150042
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (5d3v.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (5d3v.pdb2.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 5D3V
  • CSU: Contacts of Structural Units for 5D3V
  • Structure Factors (720 Kb)
  • Retrieve 5D3V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D3V from S2C, [Save to disk]
  • Re-refined 5d3v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D3V 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 5D3V
  • 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
  • Fold representative 5d3v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d3v_A] [5d3v] [5d3v_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D3V: [PH ] by SMART
  • Other resources with information on 5D3V
  • Community annotation for 5D3V at PDBWiki (http://pdbwiki.org)

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