5V6V Hydrolase Hydrolase Inhibitor date Mar 17, 2017
title Crystal Structure Of Small Molecule Aziridine 3 Covalently B Ras G12c
authors L.M.Mcgregor, M.Jenkins, C.Kerwin, J.E.Burke, K.M.Shokat
compound source
Molecule: Gtpase Kras
Chain: A, B
Synonym: K-Ras 2,Ki-Ras,C-K-Ras,C-Ki-Ras
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kras, Kras2, Rask2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.168 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.230 39.170 62.340 77.34 81.44 76.86
method X-Ray Diffractionresolution 1.72 Å
ligand 8YA, CA, GDP, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceExpanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes., McGregor LM, Jenkins ML, Kerwin C, Burke JE, Shokat KM, Biochemistry. 2017 Jun 27;56(25):3178-3183. doi: 10.1021/acs.biochem.7b00271., Epub 2017 Jun 16. PMID:28621541
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (5v6v.pdb1.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 5V6V
  • CSU: Contacts of Structural Units for 5V6V
  • Structure Factors (1311 Kb)
  • Retrieve 5V6V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V6V from S2C, [Save to disk]
  • Re-refined 5v6v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5V6V 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 5V6V
  • 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: [5v6v_B] [5v6v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5V6V
  • Community annotation for 5V6V at PDBWiki (http://pdbwiki.org)

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