3KUD Gtp Binding Protein Transferase date Nov 27, 2009
title Complex Of Ras-Gdp With Rafrbd(A85k)
authors D.Filchtinski, O.Sharabi, A.Rueppel, I.R.Vetter, C.Herrmann, J.M.
compound source
Molecule: Gtpase Hras
Chain: A
Fragment: Unp Residues 1-166
Synonym: Transforming Protein P21, P21ras, H-Ras-1, C-H-Ras Gtpase Hras, N-Terminally Processed;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hras, Hras1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Raf Proto-Oncogene Serinethreonine-Protein Kinas
Chain: B
Fragment: Unp Residues 51-131
Synonym: C-Raf, Craf, Raf-1
Ec: 2.7.11.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Raf1, Raf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.237 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.130 91.130 277.980 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.15 Å
ligand GDP, MG enzyme Transferase E.C.2.7.11.1 BRENDA
note 3KUD (Molecule of the Month:pdb195)
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceWhat makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf., Filchtinski D, Sharabi O, Ruppel A, Vetter IR, Herrmann C, Shifman JM, J Mol Biol. 2010 Jun 11;399(3):422-35. Epub 2010 Mar 31. PMID:20361980
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3kud.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 3KUD
  • CSU: Contacts of Structural Units for 3KUD
  • Structure Factors (197 Kb)
  • Retrieve 3KUD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KUD from S2C, [Save to disk]
  • Re-refined 3kud structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KUD 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 3KUD
  • 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
  • 3D motif for 3KUD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kud] [3kud_B] [3kud_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KUD: [RAS] [RBD ] by SMART
  • Other resources with information on 3KUD
  • Community annotation for 3KUD 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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