3MJG Hormone Transferase date Apr 12, 2010
title The Structure Of A Platelet Derived Growth Factor Receptor C
authors A.H.R.Shim, X.He
compound source
Molecule: Platelet-Derived Growth Factor Subunit B
Chain: A, B
Fragment: Unp Residues 21-185
Synonym: Pdgf Subunit B, Platelet-Derived Growth Factor B C Platelet-Derived Growth Factor Beta Polypeptide, Pdgf-2, Pr Oncogene C-Sis;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdgf2, Pdgfb, Sis
Expression_system: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Kidney-293 Cells

Molecule: Beta-Type Platelet-Derived Growth Factor Receptor
Chain: X, Y
Fragment: Unp Residues 33-314
Synonym: Pdgf-R-Beta, Cd140 Antigen-Like Family Member B
Ec: 2.7.10.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdgfrb
Expression_system: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Kidney-293 Cells
symmetry Space Group: P 21 21 21
R_factor 0.237 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.470 116.820 134.150 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand NAG, NDG enzyme Transferase E.C.2.7.10.1 BRENDA
note 3MJG is a representative structure
Primary referenceStructures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex., Shim AH, Liu H, Focia PJ, Chen X, Lin PC, He X, Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11307-12. Epub 2010 Jun 2. PMID:20534510
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (3mjg.pdb1.gz) 149 Kb
  • Biological Unit Coordinates (3mjg.pdb2.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 3MJG
  • CSU: Contacts of Structural Units for 3MJG
  • Structure Factors (474 Kb)
  • Retrieve 3MJG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MJG from S2C, [Save to disk]
  • Re-refined 3mjg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MJG 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 3MJG
  • 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 3MJG, from MSDmotif at EBI
  • Fold representative 3mjg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mjg] [3mjg_Y] [3mjg_B] [3mjg_A] [3mjg_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3MJG: [IG] [IGc2] [PDGF ] by SMART
  • Other resources with information on 3MJG
  • Community annotation for 3MJG 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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