1RV6 Hormone Growth Factor Receptor date Dec 12, 2003
title Crystal Structure Of Plgf In Complex With Domain 2 Of Vegfr1
authors H.W.Christinger, G.Fuh, A.M.De Vos, C.Wiesmann
compound source
Molecule: Placenta Growth Factor (Plgf)
Chain: V, W
Fragment: Receptor Binding Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Flt1 Protein
Chain: X, Y
Fragment: Domain-2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.281 71.979 115.346 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand B3P enzyme
related structures by homologous chain: 1FLT, 1FZV, 1QTY
Gene
Ontology
ChainFunctionProcessComponent
W, V


X, Y


Primary referenceThe crystal structure of placental growth factor in complex with domain 2 of vascular endothelial growth factor receptor-1., Christinger HW, Fuh G, de Vos AM, Wiesmann C, J Biol Chem 2004 Mar 12;279(11):10382-8. Epub 2003 Dec 18. PMID:14684734
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (1rv6.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 1RV6
  • CSU: Contacts of Structural Units for 1RV6
  • Likely Quarternary Molecular Structure file(s) for 1RV6
  • Structure Factors (111 Kb)
  • Retrieve 1RV6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RV6 from S2C, [Save to disk]
  • Re-refined 1rv6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RV6 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 1RV6
  • 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 1RV6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rv6v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1rv6w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1rv6x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1rv6y_, region Y [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rv6] [1rv6_V] [1rv6_X] [1rv6_Y] [1rv6_W]
  • SWISS-PROT database: [P49763] [P17948]
  • Domain organization of [PLGF_HUMAN] [VGFR1_HUMAN] by SWISSPFAM
  • Domains found in 1RV6: [IG] [PDGF ] by SMART
  • Other resources with information on 1RV6
  • Community annotation for 1RV6 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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