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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORM OF THE UNPHOSPHORYLATED HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3)
 
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 :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Dapk3, Apo, Death-Associated Protein Kinase 3, Zipper- Interacting Protein 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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2PGO2Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:23 , ALA A:25 , LYS A:42 , GLU A:64 , GLY A:163 , GOL A:301 , HOH A:2016 , HOH A:2037BINDING SITE FOR RESIDUE GOL A 300
2AC2SOFTWARELYS A:42 , GLU A:64 , ILE A:77 , ILE A:160 , ASP A:161 , PHE A:162 , GOL A:300 , HOH A:2016 , HOH A:2183BINDING SITE FOR RESIDUE GOL A 301
3AC3SOFTWAREILE A:209 , LEU A:210 , HOH A:2137BINDING SITE FOR RESIDUE PGO A 302
4AC4SOFTWARELYS B:42 , GLU B:64 , ILE B:77 , ILE B:160 , ASP B:161 , PHE B:162 , HOH B:2120BINDING SITE FOR RESIDUE GOL B 300
5AC5SOFTWAREPHE B:102 , ALA B:106 , ILE B:209 , LEU B:210BINDING SITE FOR RESIDUE PGO B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A6O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A6O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A6O)

(-) Exons   (0, 0)

(no "Exon" information available for 5A6O)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee..hhhhh.....hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a6o A   9 VEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAI 278
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168||     183       193       203       213       223       233       243       253       263       273     
                                                                                                                                                                                          169|                                                                                                       
                                                                                                                                                                                           175                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               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
                 5a6o B   7 SMVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKA 277
                                    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
   Legend:   → Mismatch (orange background)
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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 5A6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A6O)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a6o
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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 5a6n

(-) Related Entries Specified in the PDB File

5a6n CRYSTAL STRUCTURE OF HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3) IN COMPLEX WITH COMPOUND 2