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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF RAT PHOSPHODIESTERASE 10A
 
Authors :  J. Pandit, E. S. Marr
Date :  15 Feb 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Phosphodiesterase 10A; Zn-Binding Site, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Chappie, J. M. Humphrey, M. P. Allen, K. G. Estep, C. B. Fox, L. A. Lebel, S. Liras, E. S. Marr, F. S. Menniti, J. Pandit, C. J. Schmidt M. Tu, R. D. Williams, F. V. Yang
Discovery Of A Series Of 6, 7-Dimethoxy-4-Pyrrolidylquinazoline Pde10A Inhibitors
J. Med. Chem. V. 50 182 2007
PubMed-ID: 17228859  |  Reference-DOI: 10.1021/JM060653B

(-) Compounds

Molecule 1 - PHOSPHODIESTERASE-10A
    ChainsA
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPVL1392
    Expression System StrainSF21
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN
    GenePDE10A, PDE10A
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPDE10A2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PFJ1Ligand/Ion6,7-DIMETHOXY-4-[(3R)-3-(QUINOXALIN-2-YLOXY)PYRROLIDIN-1-YL]QUINAZOLINE
3SO41Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PFJ1Ligand/Ion6,7-DIMETHOXY-4-[(3R)-3-(QUINOXALIN-2-YLOXY)PYRROLIDIN-1-YL]QUINAZOLINE
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PFJ3Ligand/Ion6,7-DIMETHOXY-4-[(3R)-3-(QUINOXALIN-2-YLOXY)PYRROLIDIN-1-YL]QUINAZOLINE
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:95 , HOH A:187 , HOH A:250 , HOH A:264 , PRO A:471 , PHE A:472 , GLU A:473 , ASN A:474 , ARG A:510 , ARG A:558BINDING SITE FOR RESIDUE SO4 A 997
2AC2SOFTWAREHOH A:3 , HIS A:519 , HIS A:553 , ASP A:554 , ASP A:664 , MG A:9002BINDING SITE FOR RESIDUE ZN A 9001
3AC3SOFTWAREHOH A:1 , HOH A:2 , HOH A:3 , HOH A:4 , HOH A:5 , ASP A:554 , ZN A:9001BINDING SITE FOR RESIDUE MG A 9002
4AC4SOFTWAREHOH A:85 , HOH A:249 , PHE A:629 , LEU A:665 , VAL A:668 , TYR A:683 , MET A:703 , GLN A:716 , GLY A:718 , PHE A:719 , ALA A:722 , VAL A:723BINDING SITE FOR RESIDUE PFJ A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OVY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OVY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OVY)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE10_RAT563-574  1A:553-564
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE10_RAT563-574  1A:553-564
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE10_RAT563-574  3A:553-564

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4ENSRNOT000000434744ENSRNOE00000249346chr1:46589078-46588743336PDE10_RAT1-23230--
1.8ENSRNOT000000434748ENSRNOE00000113838chr1:46489570-46489442129PDE10_RAT23-66440--
1.9ENSRNOT000000434749ENSRNOE00000113971chr1:46469438-4646941029PDE10_RAT66-75100--
1.10ENSRNOT0000004347410ENSRNOE00000111664chr1:46460575-46460455121PDE10_RAT76-116410--
1.11ENSRNOT0000004347411ENSRNOE00000107317chr1:46459115-4645906650PDE10_RAT116-132170--
1.12ENSRNOT0000004347412ENSRNOE00000111917chr1:46434039-46433899141PDE10_RAT133-179470--
1.13ENSRNOT0000004347413ENSRNOE00000107591chr1:46432311-46432156156PDE10_RAT180-231520--
1.14ENSRNOT0000004347414ENSRNOE00000107720chr1:46430918-4643086851PDE10_RAT232-248170--
1.15ENSRNOT0000004347415ENSRNOE00000107853chr1:46430355-4643029759PDE10_RAT249-268200--
1.16ENSRNOT0000004347416ENSRNOE00000107981chr1:46428492-4642844152PDE10_RAT268-285180--
1.17ENSRNOT0000004347417ENSRNOE00000108113chr1:46425955-46425813143PDE10_RAT286-333480--
1.18ENSRNOT0000004347418ENSRNOE00000108232chr1:46423782-4642369093PDE10_RAT333-364320--
1.19ENSRNOT0000004347419ENSRNOE00000108353chr1:46421634-46421448187PDE10_RAT364-426630--
1.20ENSRNOT0000004347420ENSRNOE00000108481chr1:46413380-46413238143PDE10_RAT427-474481A:453-46412
1.21ENSRNOT0000004347421ENSRNOE00000108623chr1:46412407-4641232484PDE10_RAT474-502291A:464-49229
1.22ENSRNOT0000004347422ENSRNOE00000112176chr1:46410141-46409991151PDE10_RAT502-552511A:492-54251
1.23ENSRNOT0000004347423ENSRNOE00000112438chr1:46407274-46407119156PDE10_RAT553-604521A:543-59452
1.24ENSRNOT0000004347424ENSRNOE00000112694chr1:46405154-46404982173PDE10_RAT605-662581A:595-65258
1.25ENSRNOT0000004347425ENSRNOE00000109171chr1:46400108-46399997112PDE10_RAT662-699381A:652-68938
1.26ENSRNOT0000004347426ENSRNOE00000109311chr1:46397919-4639783981PDE10_RAT700-726271A:690-71627
1.27ENSRNOT0000004347427ENSRNOE00000109437chr1:46396042-4639595489PDE10_RAT727-756301A:717-74630
1.28bENSRNOT0000004347428bENSRNOE00000358624chr1:46393765-46392900866PDE10_RAT756-794391A:746-75712

(-) Sequences/Alignments

Asymmetric 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:305
 aligned with PDE10_RAT | Q9QYJ6 from UniProtKB/Swiss-Prot  Length:794

    Alignment length:305
                                   472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762     
            PDE10_RAT   463 NLPARICRDIELFHFDIGPFENMWPGIFVYMIHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNNGLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLHNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLNQWEKVIR 767
               SCOP domains d2ovya_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20   ---------------------------Exon 1.22  PDB: A:492-542 UniProt: 502-552         Exon 1.23  PDB: A:543-594 UniProt: 553-604          Exon 1.24  PDB: A:595-652 UniProt: 605-662                -------------------------------------Exon 1.26  PDB: A:690-716  Exon 1.27  PDB: A:717-746     ----------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.21  PDB: A:464-492    ---------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.25  PDB: A:652-689             --------------------------------------------------------Exon 1.28b   Transcript 1 (2)
                 2ovy A 453 NLPARICRDIELFHFDIGPFENMWPGIFVYMIHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNNGLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLHNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLNQWEKVIR 757
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OVY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OVY)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDE10_RAT | Q9QYJ6)
molecular function
    GO:0047555    3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0004118    cGMP-stimulated cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0043949    regulation of cAMP-mediated signaling    Any process which modulates the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0010738    regulation of protein kinase A signaling    Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE10_RAT | Q9QYJ62o8h 2ovv 3hqw 3hqy 3hqz 3hr1 3lxg 3qpn 3qpo 3qpp

(-) Related Entries Specified in the PDB File

2o8h 2ovv