Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF THE CATALYTIC DOMAIN OF CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4C
 
Authors :  S. Ramadevi, S. Sunitatajne
Date :  06 Jun 02  (Deposition) - 26 Jun 02  (Release) - 20 Nov 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ramadevi, S. Sunitatajne
Theoretical Model Of The Catalytic Domain Of Camp-Specific 3', 5'-Cyclic Phosphodiesterase 4C
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4C
    ChainsA
    EC Number3.1.4.17
    FragmentRESIDUES 1-344
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LXU)

(-) Sites  (0, 0)

(no "Site" information available for 1LXU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Theoretical Model
No.Residues
1His A:312 -Pro A:313
2Asn A:342 -Pro A:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034374R344QPDE4C_HUMANPolymorphism2229228AR39Q
2UniProtVAR_061497R344WPDE4C_HUMANPolymorphism11879710AR39W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4C_HUMAN428-439  1A:123-134

(-) Exons   (8, 8)

Theoretical Model (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003555021ENSE00001547443chr19:18359010-1835898130PDE4C_HUMAN-00--
1.2ENST000003555022ENSE00002195298chr19:18344210-18343760451PDE4C_HUMAN1-81810--
1.5ENST000003555025ENSE00001608122chr19:18333133-18332942192PDE4C_HUMAN81-145650--
1.6ENST000003555026ENSE00001744322chr19:18332107-1833207137PDE4C_HUMAN145-157130--
1.7ENST000003555027ENSE00001650541chr19:18331988-1833191574PDE4C_HUMAN158-182250--
1.8ENST000003555028ENSE00001124405chr19:18331733-1833168450PDE4C_HUMAN182-199180--
1.9ENST000003555029ENSE00001124400chr19:18331325-18331213113PDE4C_HUMAN199-236380--
1.10ENST0000035550210ENSE00001124514chr19:18331129-1833103694PDE4C_HUMAN237-268320--
1.11ENST0000035550211ENSE00000690236chr19:18330207-18330044164PDE4C_HUMAN268-322551A:1-1717
1.12ENST0000035550212ENSE00000690235chr19:18329848-1832975099PDE4C_HUMAN323-355331A:18-5033
1.13ENST0000035550213ENSE00000690234chr19:18329308-18329144165PDE4C_HUMAN356-410551A:51-10555
1.14ENST0000035550214ENSE00000690232chr19:18329058-18328959100PDE4C_HUMAN411-444341A:106-13934
1.15ENST0000035550215ENSE00000690229chr19:18327705-18327551155PDE4C_HUMAN444-495521A:139-19052
1.16ENST0000035550216ENSE00000690225chr19:18324300-18324178123PDE4C_HUMAN496-536411A:191-23141
1.17ENST0000035550217ENSE00001773479chr19:18322751-18322569183PDE4C_HUMAN537-597611A:232-29261
1.18ENST0000035550218ENSE00001399226chr19:18322086-183187713316PDE4C_HUMAN598-7121151A:293-34452

(-) Sequences/Alignments

Theoretical Model
   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:344
 aligned with PDE4C_HUMAN | Q08493 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:344
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645    
          PDE4C_HUMAN   306 TVPRFGVQTDQEEQLAKELEDTNKWGLDVFKVAELSGNRPLTAIIFSIFQERDLLKTFQIPADTLATYLLMLEGHYHANVAYHNSLHAADVAQSTHVLLATPALEAVFTDLEILAALFASAIHDVDHPGVSNQFLINTNSELALMYNDASVLENHHLAVGFKLLQAENCDIFQNLSAKQRLSLRRMVIDMVLATDMSKHMNLLADLKTMVETKKVTSLGVLLLDNYSDRIQVLQNLVHCADLSNPTKPLPLYRQWTDRIMAEFFQQGDRERESGLDISPMCDKHTASVEKSQVGFIDYIAHPLWETWADLVHPDAQDLLDTLEDNREWYQSKIPRSPSDLTNPE 649
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.11        Exon 1.12  PDB: A:18-50          Exon 1.13  PDB: A:51-105 UniProt: 356-410              Exon 1.14  PDB: A:106-139         ---------------------------------------------------Exon 1.16  PDB: A:191-231                Exon 1.17  PDB: A:232-292 UniProt: 537-597                   Exon 1.18  PDB: A:293-344 UniProt: 598-712           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------Exon 1.15  PDB: A:139-190 UniProt: 444-495          ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1lxu A   1 TVPRFGVQTDQEEQLAKELEDTNKWGLDVFKVAELSGNRPLTAIIFSIFQERDLLKTFQIPADTLATYLLMLEGHYHANVAYHNSLHAADVAQSTHVLLATPALEAVFTDLEILAALFASAIHDVDHPGVSNQFLINTNSELALMYNDASVLENHHLAVGFKLLQAENCDIFQNLSAKQRLSLRRMVIDMVLATDMSKHMNLLADLKTMVETKKVTSLGVLLLDNYSDRIQVLQNLVHCADLSNPTKPLPLYRQWTDRIMAEFFQQGDRERESGLDISPMCDKHTASVEKSQVGFIDYIAHPLWETWADLVHPDAQDLLDTLEDNREWYQSKIPRSPSDLTNPE 344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    

   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  (0, 0)

(no "SCOP Domain" information available for 1LXU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LXU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LXU)

(-) Gene Ontology  (14, 14)

Theoretical Model(hide GO term definitions)
Chain A   (PDE4C_HUMAN | Q08493)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-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:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0046676    negative regulation of insulin secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

 Visualization

(-) Interactive Views

Theoretical Model
  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
(no "Ligands, Modified Residues, Ions" information available for 1lxu)
 
  Sites
(no "Sites" information available for 1lxu)
 
  Cis Peptide Bonds
    Asn A:342 - Pro A:343   [ RasMol ]  
    His A:312 - Pro A:313   [ RasMol ]  
 

(-) 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
  1lxu
    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
  PDE4C_HUMAN | Q08493
    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
  PDE4C_HUMAN | Q08493
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4C_HUMAN | Q084932qym

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LXU)