4DSN Hydrolase date Feb 19, 2012
title Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Sos-Mediated Nucleotide Exchange Activity
authors A.Oh, T.Maurer, L.S.Garrenton, K.Pitts, D.J.Anderson, N.J.Skelton B.P.Fauber, B.Pan, S.Malek, D.Stokoe, M.Ludlam, K.K.Bowman, J.Wu, A.M.Giannetti, M.A.Starovasnik, I.Mellman, P.K.Jackson, J.Ruldo G.Fang, W.Wang
compound source
Molecule: Gtpase Kras, Isoform 2b
Chain: A
Synonym: Kras 4b, K-Ras 2, Ki-Ras, C-K-Ras, C-Ki-Ras, Gtpas Terminally Processed;
Ec: 3.6.-.-
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: H 3
R_factor 0.165 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.638 78.638 77.353 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.03 Å
ligand EDO, GCP, MG enzyme Hydrolase E.C.3.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSmall-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity., Maurer T, Garrenton LS, Oh A, Pitts K, Anderson DJ, Skelton NJ, Fauber BP, Pan B, Malek S, Stokoe D, Ludlam MJ, Bowman KK, Wu J, Giannetti AM, Starovasnik MA, Mellman I, Jackson PK, Rudolph J, Wang W, Fang G, Proc Natl Acad Sci U S A. 2012 Mar 19. PMID:22431598
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (4dsn.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 4DSN
  • CSU: Contacts of Structural Units for 4DSN
  • Structure Factors (216 Kb)
  • Retrieve 4DSN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DSN from S2C, [Save to disk]
  • Re-refined 4dsn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DSN 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 4DSN
  • 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 4DSN, from MSDmotif at EBI
  • Fold representative 4dsn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dsn_A] [4dsn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4DSN with the sequences similar proteins can be viewed for 4DSN'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 4DSN
  • Community annotation for 4DSN at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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