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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 12
 
Authors :  S. Y. Kim, T. Kohno, T. Mori, K. Kitano, T. Hakoshima
Date :  30 Apr 15  (Deposition) - 17 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Diesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Y. Kim, T. Kohno, T. Mori, K. Kitano, T. Hakoshima
Crystal Structure Of Human Phosphodiesterase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2',5'-PHOSPHODIESTERASE 12
    Chains: A
    EC Number: 3.1.4.-, 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 154-609
    Gene: PDE12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 2-PDE,MITOCHONDRIAL DEADENYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:351 , HOH A:823 , HOH A:865 , HOH A:881 , HOH A:892 , HOH A:1145binding site for residue MG A 701
2AC2SOFTWAREHIS A:456 , ASP A:496 , ASN A:498 , HOH A:865binding site for residue MG A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZKF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:590 -Pro A:591

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZKF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZKF)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZKF)

(-) 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh......eeeeee....ee.......eeeee..hhhhheeeeeee....................hhh.eee..........hhhhh...eeeeee..........eeee....ee......hhhhhhhhh.......eeeeeeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhh.eeeeeee....eeeeeee...eeeeee..eehhhhhhhh..hhhhhhhhh.hhhhhhhhhh...eeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhee...hhhhhh..........ee....eee........eee..eee..eeeeee...eeeeee....hhhhhh................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zkf A 148 GIDPFTKYKVERNPPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAEPEVGVPSSLSPSSPSSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGHSRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVINGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCLDYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK 609
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607
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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 4ZKF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZKF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZKF)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  4zkf
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE12_HUMAN | Q6L8Q7: 4z0v 4z2b

(-) Related Entries Specified in the PDB File

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