2XV7 Hormone date Oct 23, 2010
title Crystal Structure Of Vascular Endothelial Growth Factor D
authors V.M.Leppanen, M.Jeltsch, A.Anisimov, D.Tvorogov, K.Aho, N.Kalkki P.Toivanen, S.Yla-Herttuala, K.Ballmer-Hofer, K.Alitalo
compound source
Molecule: Vascular Endothelial Growth Factor D
Chain: A
Fragment: Vegf Homology Domain, Residues 92-195
Synonym: C-Fos-Induced Growth Factor, Vegf-D, Figf
Engineered: Yes
Mutation: Yes
Other_details: N-Glycosylation At Asn155 And Asn185.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 61 2 2
R_factor 0.255 R_Free 0.333
length a length b length c angle alpha angle beta angle gamma
95.720 95.720 70.940 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand BMA, MAN, NAG enzyme

Primary referenceStructural determinants of vascular endothelial growth factor-D - receptor binding and specificity., Leppanen VM, Jeltsch M, Anisimov A, Tvorogov D, Aho K, Kalkkinen N, Toivanen P, Yla-Herttuala S, Ballmer-Hofer K, Alitalo K, Blood. 2010 Dec 8. PMID:21148085
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2xv7.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2XV7
  • CSU: Contacts of Structural Units for 2XV7
  • Structure Factors (35 Kb)
  • Retrieve 2XV7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XV7 from S2C, [Save to disk]
  • Re-refined 2xv7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XV7 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 2XV7
  • 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 2XV7, from MSDmotif at EBI
  • Fold representative 2xv7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xv7] [2xv7_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XV7: [GHA] [PDGF ] by SMART
  • Other resources with information on 2XV7
  • Community annotation for 2XV7 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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