5JI1 Cytokine date Apr 21, 2016
title Crystal Structure Of Gdf8
authors R.G.Walker, T.B.Thompson
compound source
Molecule: Growthdifferentiation Factor 8
Chain: A, B
Fragment: Unp Residues 268-376
Synonym: Gdf-8,Myostatin
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mstn, Gdf8
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell: Cho
symmetry Space Group: P 21 21 21
R_factor 0.235 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
29.606 77.739 119.544 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for potency differences between GDF8 and GDF11., Walker RG, Czepnik M, Goebel EJ, McCoy JC, Vujic A, Cho M, Oh J, Aykul S, Walton KL, Schang G, Bernard DJ, Hinck AP, Harrison CA, Martinez-Hackert E, Wagers AJ, Lee RT, Thompson TB, BMC Biol. 2017 Mar 3;15(1):19. doi: 10.1186/s12915-017-0350-1. PMID:28257634
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5ji1.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 5JI1
  • CSU: Contacts of Structural Units for 5JI1
  • Structure Factors (276 Kb)
  • Retrieve 5JI1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JI1 from S2C, [Save to disk]
  • Re-refined 5ji1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JI1 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 5JI1
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ji1_B] [5ji1_A] [5ji1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JI1
  • Community annotation for 5JI1 at PDBWiki (http://pdbwiki.org)

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