3WF6 Transferase Transferase Inhibitor date Jul 17, 2013
title Crystal Structure Of S6k1 Kinase Domain In Complex With A Pyrazolopyrimidine Derivative 4-[4-(1h-Indol-3-Yl)-3,6- Dihydropyridin-1(2h)-Yl]-1h-Pyrazolo[3,4-D]Pyrimidine
authors H.Niwa, M.Shirouzu, S.Yokoyama
compound source
Molecule: Ribosomal Protein S6 Kinase Beta-1
Chain: A
Fragment: Unp Residues 78-399
Synonym: S6k-Beta-1, S6k1, 70 Kda Ribosomal Protein S6 Kina Ribosomal Protein S6 Kinase I, Serinethreonine-Protein Kin P70 Ribosomal S6 Kinase Alpha;
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps6kb1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 41 21 2
R_factor 0.195 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.073 69.073 144.983 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand FZ9, TPO, ZN enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of the S6K1 kinase domain in complexes with inhibitors., Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S, J Struct Funct Genomics. 2014 Sep;15(3):153-164. Epub 2014 Jul 31. PMID:25078151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (3wf6.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 3WF6
  • CSU: Contacts of Structural Units for 3WF6
  • Structure Factors (1138 Kb)
  • Retrieve 3WF6 in mmCIF format [Save to disk]
  • Re-refined 3wf6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WF6 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 3WF6
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3WF6, from MSDmotif at EBI
  • Fold representative 3wf6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wf6_A] [3wf6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WF6: [S_TK_X] [S_TKc ] by SMART
  • Other resources with information on 3WF6
  • Community annotation for 3WF6 at PDBWiki (http://pdbwiki.org)

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