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(-) Description

Title :  THEORETICAL MODEL OF THE CATALYTIC DOMAIN OF 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1B
 
Authors :  S. Sunitatajne, S. Ramadevi, M. Praveenkumar
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. Sunitatajne, S. Ramadevi, M. Praveenkumar
Theoretical Model Of The Catalytic Domain Of 3', 5'-Cyclic Nucleotide Phosphodiesterase 1B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1B
    ChainsA
    EC Number3.1.4.17
    FragmentRESIDUES 1-304
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCALCIUM/CALMODULIN-DEPENDENT 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1B

 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 1LXR)

(-) Sites  (0, 0)

(no "Site" information available for 1LXR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Glu A:284 -Lys A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE1B_HUMAN263-274  1A:106-117

(-) Exons   (10, 10)

Theoretical Model (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002430521ENSE00001183864chr12:54943404-54943556153PDE1B_HUMAN-00--
1.2ENST000002430522ENSE00001147374chr12:54943644-54943769126PDE1B_HUMAN1-38380--
1.4ENST000002430524ENSE00000838447chr12:54960758-54960871114PDE1B_HUMAN38-76390--
1.5ENST000002430525ENSE00000920047chr12:54962968-54963150183PDE1B_HUMAN76-137620--
1.6ENST000002430526ENSE00000920048chr12:54963330-5496339667PDE1B_HUMAN137-159231A:1-22
1.7ENST000002430527ENSE00000920049chr12:54964025-54964141117PDE1B_HUMAN160-198391A:3-4139
1.8ENST000002430528ENSE00000920050chr12:54966385-54966525141PDE1B_HUMAN199-245471A:42-8847
1.9ENST000002430529ENSE00000920051chr12:54966932-54967032101PDE1B_HUMAN246-279341A:89-12234
1.10ENST0000024305210ENSE00000920052chr12:54967139-54967264126PDE1B_HUMAN279-321431A:122-16443
1.11ENST0000024305211ENSE00000920053chr12:54967392-54967493102PDE1B_HUMAN321-355351A:164-19835
1.12ENST0000024305212ENSE00000920054chr12:54968882-54969002121PDE1B_HUMAN355-395411A:198-23841
1.13ENST0000024305213ENSE00000920055chr12:54969335-5496941682PDE1B_HUMAN396-423281A:239-26628
1.14ENST0000024305214ENSE00000920056chr12:54969776-54969884109PDE1B_HUMAN423-459371A:266-30237
1.15ENST0000024305215ENSE00000920057chr12:54970355-54970485131PDE1B_HUMAN459-503451A:302-3043
1.16ENST0000024305216ENSE00000920058chr12:54971009-54971129121PDE1B_HUMAN503-536340--
1.17ENST0000024305217ENSE00001147267chr12:54971644-549730231380PDE1B_HUMAN-00--

(-) 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:304
 aligned with PDE1B_HUMAN | Q01064 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:304
                                   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    
          PDE1B_HUMAN   158 LKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQPLADEDSKSKNQPSFQ 461
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.7  PDB: A:3-41 UniProt: 160-198 Exon 1.8  PDB: A:42-88 UniProt: 199-245        ---------------------------------Exon 1.10  PDB: A:122-164 UniProt: 279-321 ---------------------------------Exon 1.12  PDB: A:198-238                Exon 1.13  PDB: A:239-266   -----------------------------------1.1 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.9  PDB: A:89-122           -----------------------------------------Exon 1.11  PDB: A:164-198          -------------------------------------------------------------------Exon 1.14  PDB: A:266-302            -- Transcript 1 (2)
                 1lxr A   1 LKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQPLADEDSKSKNQPSFQ 304
                                    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    

   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 1LXR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Theoretical Model(hide GO term definitions)
Chain A   (PDE1B_HUMAN | Q01064)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    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:0048101    calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate. The reaction is calmodulin and calcium-sensitive.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004117    calmodulin-dependent cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is regulated by calmodulin.
    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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0097011    cellular response to granulocyte macrophage colony-stimulating factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a granulocyte macrophage colony-stimulating factor stimulus.
    GO:0036006    cellular response to macrophage colony-stimulating factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a macrophage colony-stimulating factor stimulus.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0030224    monocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
    GO:0042053    regulation of dopamine metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dopamine.
    GO:0001505    regulation of neurotransmitter levels    Any process that modulates levels of neurotransmitter.
    GO:0001975    response to amphetamine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0042428    serotonin metabolic process    The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
    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.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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    Glu A:284 - Lys A:285   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE1B_HUMAN | Q010641taz 4npv 4npw 5b25 5uoy 5up0

(-) Related Entries Specified in the PDB File

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