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(-) Description

Title :  CRYSTAL STRUCTURE OF DAPK1-KAEMPFEROL COMPLEX IN THE PRESENCE OF IODIDE IONS.
 
Authors :  T. Yokoyama, M. Mizuguchi
Date :  10 Jun 15  (Deposition) - 07 Oct 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Death-Associated Protein Kinase 1, Serine/Threonine Protein Kinase, Natural Flavonoid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yokoyama, Y. Kosaka, M. Mizuguchi
Structural Insight Into The Interactions Between Death-Associated Protein Kinase 1 And Natural Flavonoids.
J. Med. Chem. V. 58 7400 2015
PubMed-ID: 26322379  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00893

(-) Compounds

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 1
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-285
    Gene: DAPK1, DAPK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAP KINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1IOD9Ligand/IonIODIDE ION
2KMP1Ligand/Ion3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:19 , GLY A:20 , SER A:21 , GLY A:22 , VAL A:27 , ALA A:40 , LYS A:42 , GLU A:94 , LEU A:95 , VAL A:96 , MET A:146 , ILE A:160 , ASP A:161 , HOH A:464binding site for residue KMP A 300
02AC2SOFTWARELYS A:42 , ASP A:161 , IOD A:302binding site for residue IOD A 301
03AC3SOFTWARELYS A:42 , LEU A:93 , ASP A:161 , IOD A:301binding site for residue IOD A 302
04AC4SOFTWAREPHE A:102 , GLU A:143 , IOD A:304binding site for residue IOD A 303
05AC5SOFTWAREPHE A:102 , PRO A:142 , IOD A:303binding site for residue IOD A 304
06AC6SOFTWARETHR A:225binding site for residue IOD A 305
07AC7SOFTWAREGLN A:267binding site for residue IOD A 306
08AC8SOFTWAREHIS A:131 , ILE A:266 , HOH A:598binding site for residue IOD A 307
09AC9SOFTWARELYS A:29binding site for residue IOD A 308
10AD1SOFTWAREARG A:254binding site for residue IOD A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AV3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AV3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AV3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AV3)

(-) Exons   (0, 0)

(no "Exon" information available for 5AV3)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh.eeeeeeeee...eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh..hhhhhhhhhh..........hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5av3 A   2 TVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKSLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKP 277
                                    11        21        31        41        51        61        71        81        91       101      |112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
                                                                                                                                    108|                                                                                                                                                                       
                                                                                                                                     110
   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 5AV3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AV3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AV3)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  DAPK1_HUMAN | P53355
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPK1_HUMAN | P53355: 1ig1 1jkk 1jkl 1jks 1jkt 1p4f 1wvw 1wvx 1wvy 1yr5 2w4j 2w4k 2x0g 2xuu 2xzs 2y0a 2y4p 2y4v 2yak 3dfc 3dgk 3eh9 3eha 3f5g 3f5u 3gu4 3gu5 3gu6 3gu7 3gu8 3gub 3zxt 4b4l 4pf4 4tl0 4txc 4uv0 4yo4 4ypd 5aut 5auu 5auv 5auw 5aux 5auy 5auz 5av0 5av1 5av2 5av4

(-) Related Entries Specified in the PDB File

5aut 5auu 5auv 5auw 5aux 5auy 5auz 5av0 5av1 5av2 5av4