2C7W Growth Factor date Nov 29, 2005
title Crystal Structure Of Human Vascular Endothelial Growth Facto Identification Of Amino Acids Important For Angiogeninc Act
authors S.Iyer, P.D.Scotney, A.D.Nash, K.R.Acharya
compound source
Molecule: Vascular Endothelial Growth Factor B Precursor
Chain: A, B
Synonym: Vascular Endothelial Growth Factor-B, Vegf-B, Vegf Factor;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet15b
symmetry Space Group: P 64
R_factor 0.286 R_Free 0.310
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.806 120.806 39.826 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.48 Å
ligand MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of human vascular endothelial growth factor-B: identification of amino acids important for receptor binding., Iyer S, Scotney PD, Nash AD, Ravi Acharya K, J Mol Biol. 2006 May 26;359(1):76-85. Epub 2006 Apr 17. PMID:16616187
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (2c7w.pdb1.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 2C7W
  • CSU: Contacts of Structural Units for 2C7W
  • Likely Quarternary Molecular Structure file(s) for 2C7W
  • Structure Factors (110 Kb)
  • Retrieve 2C7W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C7W from S2C, [Save to disk]
  • Re-refined 2c7w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2C7W 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 2C7W
  • 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 2C7W, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c7w_B] [2c7w_A] [2c7w]
  • SWISS-PROT database: [P49765]
  • Domain organization of [VEGFB_HUMAN] by SWISSPFAM
  • Domain found in 2C7W: [PDGF ] by SMART
    • Other resources with information on 2C7W
  • Community annotation for 2C7W 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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