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
  • Alignments of the sequence of 3MJG with the sequences similar proteins can be viewed for 3MJG's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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