5XGC Oncoprotein date Apr 13, 2017
title Crystal Structure Of Smggds-558
authors H.Shimizu, S.Toma-Fukai, T.Shimizu
compound source
Molecule: Rap1 Gtpase-Gdp Dissociation Stimulator 1
Chain: A
Fragment: Unp Residues 61-558
Synonym: Exchange Factor Smggds,Smg Gds Protein,Smg P21 Sti Gdpgtp Exchange Protein;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rap1gds1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.215 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
194.330 51.115 52.444 90.00 92.77 90.00
method X-Ray Diffractionresolution 2.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding., Shimizu H, Toma-Fukai S, Saijo S, Shimizu N, Kontani K, Katada T, Shimizu T, J Biol Chem. 2017 Aug 11;292(32):13441-13448. doi: 10.1074/jbc.M117.792556. Epub , 2017 Jun 19. PMID:28630045
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (5xgc.pdb1.gz) 70 Kb
  • CSU: Contacts of Structural Units for 5XGC
  • Structure Factors (847 Kb)
  • Retrieve 5XGC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XGC from S2C, [Save to disk]
  • Re-refined 5xgc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5XGC 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 5XGC
  • 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: [5xgc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XGC
  • Community annotation for 5XGC at PDBWiki (http://pdbwiki.org)

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