4D9T Transferase Transferase Inhibitor date Jan 12, 2012
title Rsk2 C-Terminal Kinase Domain With Inhibitor (E)-Methyl 3-(4 (3-Hydroxypropyl)-5-P-Tolyl-7h-Pyrrolo[2,3-D]Pyrimidin-6-Yl Cyanoacrylate
authors I.M.Serafimova, M.A.Pufall, S.Krishnan, K.Duda, M.S.Cohen, R.L.Ma J.M.Mcfarland, R.M.Miller, M.Frodin, J.Taunton
compound source
Molecule: Ribosomal Protein S6 Kinase Alpha-3
Chain: A
Fragment: C-Terminal Kinase Domain, Unp Residues 399-740
Synonym: S6k-Alpha-3, 90 Kda Ribosomal Protein S6 Kinase 3, 3, P90rsk3, Insulin-Stimulated Protein Kinase 1, Ispk-1, Ma Activated Protein Kinase 1b, Mapk-Activated Protein Kinase Kinase 1b, Mapkapk-1b, Ribosomal S6 Kinase 2, Rsk-2, Pp90rs
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ispk1, Mapkapk1b, Rps6ka3, Rsk2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet46
symmetry Space Group: P 41 21 2
R_factor 0.216 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
46.700 46.700 294.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 0JG, NA enzyme Transferase E.C. BRENDA

Primary referenceReversible targeting of noncatalytic cysteines with chemically tuned electrophiles., Serafimova IM, Pufall MA, Krishnan S, Duda K, Cohen MS, Maglathlin RL, McFarland JM, Miller RM, Frodin M, Taunton J, Nat Chem Biol. 2012 Apr 1;8(5):471-6. doi: 10.1038/nchembio.925. PMID:22466421
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (4d9t.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (4d9t.pdb2.gz) 203 Kb
  • LPC: Ligand-Protein Contacts for 4D9T
  • CSU: Contacts of Structural Units for 4D9T
  • Structure Factors (96 Kb)
  • Retrieve 4D9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D9T from S2C, [Save to disk]
  • Re-refined 4d9t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D9T 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 4D9T
  • 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 4D9T, from MSDmotif at EBI
  • Fold representative 4d9t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d9t] [4d9t_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4D9T: [S_TKc ] by SMART
  • Other resources with information on 4D9T
  • Community annotation for 4D9T at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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