2X1W Hormone Signaling Protein date Jan 08, 2010
title Crystal Structure Of Vegf-C In Complex With Domains 2 And 3
authors V.M.Leppanen, A.E.Prota, M.Jeltsch, A.Anisimov, N.Kalkkinen, T.St H.Lankinen, A.Goldman, K.Ballmer-Hofer, K.Alitalo
compound source
Molecule: Vascular Endothelial Growth Factor C
Chain: A, B, C, D
Fragment: Vegf Homology Domain, Residues 112-215
Synonym: Vegf-C, Vascular Endothelial Growth Factor-Related Vrp, Flt4 Ligand, Flt4-L;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac

Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: L, M, N, O
Fragment: Ig-Like Domains 2 And 3, Residues 120-326
Synonym: Vegf Receptor 2, Vegfr-2, Kinase Insert Domain Rec Protein-Tyrosine Kinase Receptor Flk-1, Cd309, Flk-1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 21 21 21
R_factor 0.227 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.750 123.830 211.831 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand BMA, CS, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


O, M, N, L


Primary referenceStructural determinants of growth factor binding and specificity by VEGF receptor 2., Leppanen VM, Prota AE, Jeltsch M, Anisimov A, Kalkkinen N, Strandin T, Lankinen H, Goldman A, Ballmer-Hofer K, Alitalo K, Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2425-30. PMID:20145116
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (405 Kb) [Save to disk]
  • Biological Unit Coordinates (2x1w.pdb1.gz) 195 Kb
  • Biological Unit Coordinates (2x1w.pdb2.gz) 201 Kb
  • LPC: Ligand-Protein Contacts for 2X1W
  • CSU: Contacts of Structural Units for 2X1W
  • Structure Factors (419 Kb)
  • Retrieve 2X1W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X1W from S2C, [Save to disk]
  • Re-refined 2x1w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X1W 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 2X1W
  • 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 2X1W, from MSDmotif at EBI
  • Fold representative 2x1w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x1w_A] [2x1w_L] [2x1w_M] [2x1w_B] [2x1w_N] [2x1w_D] [2x1w_O] [2x1w] [2x1w_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2X1W: [GHA] [IG] [IG_like] [PDGF ] by SMART
  • Other resources with information on 2X1W
  • Community annotation for 2X1W 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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