2XAC Transferase Signaling Protein date Mar 30, 2010
title Structural Insights Into The Binding Of Vegf-B By Vegfr-1d2: Recognition And Specificity
authors S.Iyer, P.Darley, K.R.Acharya
compound source
Molecule: Vascular Endothelial Growth Factor B
Chain: A, B
Fragment: Receptor-Binding Domain, Residues 31-129
Synonym: Vegf-B, Vegf-Related Factor, Vrf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosettagami B (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-32 Xalic

Molecule: Vascular Endothelial Growth Factor Receptor 1
Chain: C, X
Fragment: Domain 2, Residues 129-226
Synonym: Vegfr-1, Vascular Permeability Factor Receptor, Tyrosine-Protein Kinase Receptor Flt, Tyrosine-Protein Kinase Frt, Flt-1, Fms-Like Tyrosine Kinase 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Codonplus-Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1 21 1
R_factor 0.282 R_Free 0.364
length a length b length c angle alpha angle beta angle gamma
39.212 65.526 82.824 90.00 90.26 90.00
method X-Ray Diffractionresolution 2.71 Å
ligand GOL enzyme Transferase E.C. BRENDA
A, B

X, C

Primary referenceStructural insights into the binding of VEGF-B by VEGFR-1D2: Recognition and specificity., Iyer S, Darley PI, Acharya KR, J Biol Chem. 2010 May 25. PMID:20501651
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (2xac.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 2XAC
  • CSU: Contacts of Structural Units for 2XAC
  • Structure Factors (138 Kb)
  • Retrieve 2XAC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XAC from S2C, [Save to disk]
  • Re-refined 2xac structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XAC 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 2XAC
  • 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 2XAC, from MSDmotif at EBI
  • Fold representative 2xac from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xac_X] [2xac_C] [2xac] [2xac_A] [2xac_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XAC: [IG] [PDGF ] by SMART
  • Other resources with information on 2XAC
  • Community annotation for 2XAC 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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