4BSK Transferase Hormone date Jun 10, 2013
title Crystal Structure Of Vegf-C In Complex With Vegfr-3 Domains
authors V.M.Leppanen, D.Tvorogov, K.Kisko, A.E.Prota, M.Jeltsch, A.Anisim S.Markovic-Mueller, E.Stuttfeld, K.N.Goldie, K.Ballmer-Hofer, K
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 3
Chain: A
Fragment: Ligand-Binding Domains D1-2, Residues 23-229
Synonym: Vegfr-3, Fms-Like Tyrosine Kinase 4, Flt-4, Tyrosi Kinase Receptor Flt4, Vegfr-3;
Ec: 2.7.10.1
Engineered: Yes
Other_details: Covalent N-Glycosylation In Asn33, Asn104 An
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: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac1

Molecule: Vascular Endothelial Growth Factor C
Chain: C
Fragment: Vegf Homology Domain, Residues 103-215
Synonym: Vegf-C, Flt4 Ligand, Flt4-L, Vascular Endothelial Factor-Related Protein, Vrp, Vegf-C;
Engineered: Yes
Mutation: Yes
Other_details: Covalent N-Glycosylation In Asn175 And Asn20

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: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac1
symmetry Space Group: I 2 3
R_factor 0.334 R_Free 0.372
crystal
cell
length a length b length c angle alpha angle beta angle gamma
166.660 166.660 166.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.20 Å
ligand NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


C


Primary referenceStructural and mechanistic insights into VEGF receptor 3 ligand binding and activation., Leppanen VM, Tvorogov D, Kisko K, Prota AE, Jeltsch M, Anisimov A, Markovic-Mueller S, Stuttfeld E, Goldie KN, Ballmer-Hofer K, Alitalo K, Proc Natl Acad Sci U S A. 2013 Jul 22. PMID:23878260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (4bsk.pdb1.gz) 153 Kb
  • LPC: Ligand-Protein Contacts for 4BSK
  • CSU: Contacts of Structural Units for 4BSK
  • Structure Factors (48 Kb)
  • Retrieve 4BSK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BSK from S2C, [Save to disk]
  • Re-refined 4bsk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BSK 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 4BSK
  • 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 4BSK, from MSDmotif at EBI
  • Fold representative 4bsk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bsk_C] [4bsk_A] [4bsk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BSK: [GHA] [IG] [PDGF ] by SMART
  • Other resources with information on 4BSK
  • Community annotation for 4BSK at PDBWiki (http://pdbwiki.org)

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