Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A
 
Authors :  K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessing G. Bollag
Date :  18 May 04  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Pde5A (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. Hsieh, J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessinger, G. Bollag
A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases
Mol. Cell V. 15 279 2004
PubMed-ID: 15260978  |  Reference-DOI: 10.1016/J.MOLCEL.2004.07.005

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
    ChainsA
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)CODON PLUS(RIL)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GenePDE5A, PDE5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPO4 A:102 , HIS A:617 , HIS A:653 , ASP A:654 , ASP A:764BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREZN A:1 , HIS A:613 , HIS A:617 , HIS A:653 , ASP A:654 , HIS A:678 , GLU A:682 , HIS A:684 , THR A:723 , ASP A:764BINDING SITE FOR RESIDUE PO4 A 102
3AC3SOFTWAREILE A:729 , ARG A:732 , GLY A:733 , PHE A:736 , ARG A:740 , GLN A:827 , HOH A:906BINDING SITE FOR RESIDUE CIT A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T9R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T9R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T9R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664  1A:653-657

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003549601aENSE00001851914chr4:120550146-120549675472PDE5A_HUMAN1-51510--
1.4ENST000003549604ENSE00001637089chr4:120528452-120527864589PDE5A_HUMAN51-2471970--
1.5bENST000003549605bENSE00000935544chr4:120517767-12051767890PDE5A_HUMAN248-277300--
1.6ENST000003549606ENSE00000970323chr4:120488299-12048822872PDE5A_HUMAN278-301240--
1.7ENST000003549607ENSE00000970324chr4:120486565-12048647690PDE5A_HUMAN302-331300--
1.8bENST000003549608bENSE00000970325chr4:120484125-120483988138PDE5A_HUMAN332-377460--
1.9ENST000003549609ENSE00000970326chr4:120481518-12048145168PDE5A_HUMAN378-400230--
1.10ENST0000035496010ENSE00000970327chr4:120474901-120474793109PDE5A_HUMAN400-436370--
1.11aENST0000035496011aENSE00000970328chr4:120473792-12047370588PDE5A_HUMAN437-466300--
1.13ENST0000035496013ENSE00000935541chr4:120463789-120463614176PDE5A_HUMAN466-524590--
1.15bENST0000035496015bENSE00000935545chr4:120460174-12046011560PDE5A_HUMAN525-544201A:534-54411
1.18ENST0000035496018ENSE00001016848chr4:120446850-120446704147PDE5A_HUMAN545-593491A:545-59349
1.19bENST0000035496019bENSE00001016844chr4:120442215-120442090126PDE5A_HUMAN594-635421A:594-63542
1.20cENST0000035496020cENSE00001016846chr4:120440294-12044020095PDE5A_HUMAN636-667321A:636-65722
1.22ENST0000035496022ENSE00001016843chr4:120432289-12043220288PDE5A_HUMAN667-696301A:672-69625
1.23bENST0000035496023bENSE00001016840chr4:120428859-120428759101PDE5A_HUMAN697-730341A:697-73034
1.24bENST0000035496024bENSE00001016847chr4:120427087-12042701078PDE5A_HUMAN730-756271A:730-75627
1.25ENST0000035496025ENSE00001016842chr4:120425754-12042569164PDE5A_HUMAN756-777221A:756-77722
1.26aENST0000035496026aENSE00001016841chr4:120423810-12042373675PDE5A_HUMAN778-802251A:778-78912
1.27aENST0000035496027aENSE00001016845chr4:120422408-12042232584PDE5A_HUMAN803-830281A:804-83027
1.28cENST0000035496028cENSE00001890486chr4:120419893-1204155504344PDE5A_HUMAN831-875451A:831-86232

(-) 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:301
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:329
                                   543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853         
          PDE5A_HUMAN   534 EEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEK 862
               SCOP domains d1t9ra_ A: cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1t9rA00 A:534-862 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------PDEase_I-1t9rA01 A:612-850                                                                                                                                                                                                                     ------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....--------------..............hhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.15b Exon 1.18  PDB: A:545-593 UniProt: 545-593       Exon 1.19b  PDB: A:594-635                Exon 1.20c  PDB: A:636-657      -----------------------------Exon 1.23b  PDB: A:697-730        -------------------------Exon 1.25             Exon 1.26a  PDB: A:778-78Exon 1.27a  PDB: A:804-830  Exon 1.28c  PDB: A:831-862       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:672-696     ---------------------------------Exon 1.24b  PDB: A:730-756 ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1t9r A 534 EEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDH--------------LAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQ--------------LMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEK 862
                                   543       553       563       573       583       593       603       613       623       633       643       653   |     -       673       683       693       703       713       723       733       743       753       763       773       783     |   -         -|      813       823       833       843       853         
                                                                                                                                                     657            672                                                                                                                  789            804                                                          

   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/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDE5A_HUMAN | O76074)
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:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    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: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:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0046068    cGMP metabolic process    The chemical reactions and pathways involving 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:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0055118    negative regulation of cardiac muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0060282    positive regulation of oocyte development    Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0030823    regulation of cGMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
    GO:0055119    relaxation of cardiac muscle    The process in which the extent of cardiac muscle contraction is reduced.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t9r)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1t9r
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PDE5A_HUMAN | O76074
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.4.17
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PDE5A_HUMAN | O76074
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_HUMAN | O760741rkp 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2chm 2h40 2h42 2h44 2xss 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

1t9s 1taz 1tb5 1tb7 1tbb 1tbf