4RRV Transferase Transferase Inhibitor date Nov 06, 2014
title Crystal Structure Of Pdk1 In Complex With Atp And Piftide
authors T.J.Rettenmaier, J.A.Wells
compound source
Molecule: 3-Phosphoinositide-Dependent Protein Kinase 1
Chain: A
Fragment: Catalytic Domain (Unp Residues 50-359)
Synonym: Hpdk1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdk1, Pdpk1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Htb

Molecule: Serinethreonine-Protein Kinase N2
Chain: B
Fragment: Piftide (Prk2 Hydrophobic Motif, Unp Residues 969
Synonym: Pkn Gamma, Protein Kinase C-Like 2, Protein-Kinase Kinase 2;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.134 R_Free 0.163
length a length b length c angle alpha angle beta angle gamma
148.973 44.536 47.799 90.00 101.40 90.00
method X-Ray Diffractionresolution 1.41 Å
ligand ATP, GOL, SEP enzyme Transferase E.C. BRENDA

Primary referenceA small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1., Rettenmaier TJ, Sadowsky JD, Thomsen ND, Chen SC, Doak AK, Arkin MR, Wells JA, Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18590-5. doi:, 10.1073/pnas.1415365112. Epub 2014 Dec 17. PMID:25518860
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (167 Kb) [Save to disk]
  • Biological Unit Coordinates (4rrv.pdb1.gz) 161 Kb
  • LPC: Ligand-Protein Contacts for 4RRV
  • CSU: Contacts of Structural Units for 4RRV
  • Structure Factors (707 Kb)
  • Retrieve 4RRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RRV from S2C, [Save to disk]
  • Re-refined 4rrv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RRV 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 4RRV
  • 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 4RRV, from MSDmotif at EBI
  • Fold representative 4rrv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rrv_A] [4rrv] [4rrv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4RRV: [S_TKc ] by SMART
  • Other resources with information on 4RRV
  • Community annotation for 4RRV at PDBWiki (http://pdbwiki.org)

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