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(-) Description

Title :  CRYSTAL STRUCTURE OF MAPK13 COMPLEX WITH INHIBITOR
 
Authors :  T. J. Brett, C. A. Miller, Z. Yurtsever
Date :  03 Nov 15  (Deposition) - 06 Jul 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Yurtsever, D. A. Patel, D. L. Kober, A. Su, C. A. Miller, A. G. Romero, M. J. Holtzman, T. J. Brett
First Comprehensive Structural And Biophysical Analysis Of Mapk13 Inhibitors Targeting Dfg-In And Dfg-Out Binding Modes.
Biochim. Biophys. Acta V. 1860 2335 2016
PubMed-ID: 27369736  |  Reference-DOI: 10.1016/J.BBAGEN.2016.06.023

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 13
    ChainsA
    EC Number2.7.11.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainROSETTA 2 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAPK13, PRKM13, SAPK4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAPK 13,MITOGEN-ACTIVATED PROTEIN KINASE P38 DELTA,MAP KINASE P38 DELTA,STRESS-ACTIVATED PROTEIN KINASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1N171Ligand/Ion3-(4-METHYL-1H-IMIDAZOL-1-YL)-N-[4-(PYRIDIN-4-YLOXY)PHENYL]BENZAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:39 , ALA A:52 , ARG A:68 , GLU A:72 , LEU A:76 , ILE A:85 , MET A:107 , PRO A:108 , MET A:110 , LEU A:167 , ASP A:168 , PHE A:169 , LEU A:171binding site for residue N17 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EKO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:326 -Ser A:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EKO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EKO)

(-) Exons   (0, 0)

(no "Exon" information available for 5EKO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee..eeeeeeeee...eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhh.........eee............eeeee...eehhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..............hhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh................hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eko A   2 SLIRKKGFYKQDVNKTAWELPKTYVSPTHVGSGAYGSVCSAIDKRSGEKVAIKKLSRPFQSEIFAKRAYRELLLLKHMQHENVIGLLDVFTPASSLRNFYDFYLVMPFMQTDLQKIMGMEFSEEKIQYLVYQMLKGLKYIHSAGVVHRDLKPGNLAVNEDCELKILDFGLGYVVTRWYRAPEVILSWMHYNQTVDIWSVGCIMAEMLTGKTLFKGKDYLDQLTQILKVTGVPGTEFVQKLNDKAAKSYIQSLPQTPRKDFTQLFPRASPQAADLLEKMLELDVDKRLTAAQALTHPFFEPFRDPEEETEAQQPFDDSLEHEKLTVDEWKQHIYKEIVNFSP 351
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171|      190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
                                                                                                                                                                                                   171|                                                                                                                                                                          
                                                                                                                                                                                                    181                                                                                                                                                                          

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EKO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EKO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EKO)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asp A:326 - Ser A:327   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MK13_HUMAN | O152643coi 4eyj 4eym 4myg 4yno 5ekn

(-) Related Entries Specified in the PDB File

4eyj SAME MOLECULE IN COMPLEX WITH A DIFFERENT INHIBITOR
4eym SAME MOLECULE IN COMPLEX WITH A DIFFERENT INHIBITOR
4myg SAME MOLECULE WITHOUT INHIBITOR IN ACTIVE FORM
4yno SAME MOLECULE WITHOUT INHIBITOR
5ekn SAME MOLECULE IN COMPLEX WITH A DIFFERENT INHIBITOR