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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3) IN COMPLEX WITH COMPOUND 2
 
Authors :  T. Rodrigues, D. Reker, M. Welin, C. Caldera, C. Brunner, G. Gabernet, P. Schneider, B. Walse, G. Schneider
Date :  30 Jun 15  (Deposition) - 21 Oct 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Dapk3, Human Death Associated Protein Kinase 3, Dap-Like Kinase, Dlk, Zipper-Interacting Protein Kinase, Zip-Kinase, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Rodrigues, D. Reker, M. Welin, M. Caldera, C. Brunner, G. Gabernet, P. Schneider, B. Walse, G. Schneider
De Novo Fragment Design For Drug Discovery And Chemical Biology.
Angew. Chem. Int. Ed. Engl. V. 54 15079 2015
PubMed-ID: 26486226  |  Reference-DOI: 10.1002/ANIE.201508055

(-) Compounds

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 3
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROTEIN KINASE DOMAIN, UNP RESIDUES 9-289
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAP KINASE 3, DAP-LIKE KINASE, DLK, MYPT1 KINASE, ZIPPER- INTERACTING PROTEIN KINASE, ZIP-KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PGO2Ligand/IonS-1,2-PROPANEDIOL
3U7E1Ligand/Ion5-(3-SULFAMOYLPHENYL)-1H-1,2,3,4-TETRAZOL-1-IDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , LYS A:42 , ILE A:77 , ASP A:161 , HOH A:2039 , HOH A:2104 , HOH A:2183BINDING SITE FOR RESIDUE U7E A 300
2AC2SOFTWAREGLU A:100 , ASP A:103 , HIS B:73 , PRO B:74 , ILE B:76 , THR B:78 , LYS B:158 , HOH B:2037BINDING SITE FOR RESIDUE GOL A 301
3AC3SOFTWARETYR A:234 , ASP A:235 , ARG A:253BINDING SITE FOR RESIDUE PGO A 302
4AC4SOFTWAREILE A:209 , LEU A:210BINDING SITE FOR RESIDUE PGO A 303
5AC5SOFTWARELYS B:42 , GLU B:64 , ILE B:77 , ILE B:160 , ASP B:161 , PHE B:162 , HOH B:2115BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A6N)

(-) Exons   (0, 0)

(no "Exon" information available for 5A6N)

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeeeeee..eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee..hhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a6n A   8 MVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAI 278
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277 


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeeee..eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee............hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a6n B   7 SMVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAI 278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166  ||   181       191       201       211       221       231       241       251       261       271       
                                                                                                                                                                                            169|                                                                                                       
                                                                                                                                                                                             175
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  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 5A6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A6N)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a6n
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  DAPK3_HUMAN | O43293
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPK3_HUMAN | O43293: 1yrp 2j90 3bhy 3bqr 5a6o

(-) Related Entries Specified in the PDB File

5a6o CRYSTAL STRUCTURE OF THE APO FORM OF THE UNPHOSPHORYLATED HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3)