5EKN Transferase Transferase Inhibitor date Nov 03, 2015
title Crystal Structure Of Mapk13 Complex With Inhibitor
authors T.J.Brett, C.A.Miller, Z.Yurtsever
compound source
Molecule: Mitogen-Activated Protein Kinase 13
Chain: A
Synonym: Mapk 13,Mitogen-Activated Protein Kinase P38 Delta Kinase P38 Delta,Stress-Activated Protein Kinase 4;
Ec: 2.7.11.24
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mapk13, Prkm13, Sapk4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.047 70.206 92.908 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.59 Å
ligand N58 enzyme Transferase E.C.2.7.11.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • positive regulation of inter...

  • Primary referenceFirst comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes., Yurtsever Z, Patel DA, Kober DL, Su A, Miller CA, Romero AG, Holtzman MJ, Brett TJ, Biochim Biophys Acta. 2016 Jun 29. pii: S0304-4165(16)30228-8. doi:, 10.1016/j.bbagen.2016.06.023. PMID:27369736
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (5ekn.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 5EKN
  • CSU: Contacts of Structural Units for 5EKN
  • Structure Factors (317 Kb)
  • Retrieve 5EKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EKN from S2C, [Save to disk]
  • Re-refined 5ekn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EKN 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 5EKN
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ekn] [5ekn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EKN: [S_TKc ] by SMART
  • Other resources with information on 5EKN
  • Community annotation for 5EKN at PDBWiki (http://pdbwiki.org)

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