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(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEX WITH PICLAMILAST
 
Authors :  G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Date :  01 Oct 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pde4B, Piclamilast, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Structural Basis For The Activity Of Drugs That Inhibit Phosphodiesterases.
Structure V. 12 2233 2004
PubMed-ID: 15576036  |  Reference-DOI: 10.1016/J.STR.2004.10.004

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    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 OF HUMAN PHOSPHODIESTERASE 4B
    GenePDE4B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDPDE4, PDE32
 
Molecule 2 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    ChainsB
    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 OF HUMAN PHOSPHODIESTERASE 4B
    GenePDE4B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDPDE4, PDE32

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2MG2Ligand/IonMAGNESIUM ION
3PIL2Ligand/Ion3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2MG-1Ligand/IonMAGNESIUM ION
3PIL1Ligand/Ion3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2MG-1Ligand/IonMAGNESIUM ION
3PIL1Ligand/Ion3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
4ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , HOH A:1008 , HOH A:1009BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:275 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007 , HOH A:1008BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWAREHIS B:238 , HIS B:274 , ASP B:275 , ASP B:392 , HOH B:2007 , HOH B:2008BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREASP B:275 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007BINDING SITE FOR RESIDUE MG B 1002
5AC5SOFTWARETYR A:233 , HIS A:234 , THR A:345 , MET A:347 , ASP A:392 , LEU A:393 , ASN A:395 , THR A:407 , ILE A:410 , PHE A:414 , SER A:442 , GLN A:443 , PHE A:446 , HOH A:1007 , HOH A:1013 , HOH A:1040BINDING SITE FOR RESIDUE PIL A 1003
6AC6SOFTWAREHOH B:76 , TYR B:233 , HIS B:234 , THR B:345 , MET B:347 , ASP B:392 , LEU B:393 , ASN B:395 , THR B:407 , ILE B:410 , MET B:431 , GLN B:443 , PHE B:446BINDING SITE FOR RESIDUE PIL B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XM4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:463 -Pro A:464
2Gln B:463 -Pro B:464

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XM4)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4B_HUMAN446-457
 
  2A:274-285
B:274-285
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4B_HUMAN446-457
 
  1A:274-285
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4B_HUMAN446-457
 
  1-
B:274-285

(-) Exons   (8, 16)

Asymmetric Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003415172ENSE00001777645chr1:66258864-6625893168PDE4B_HUMAN-00--
1.3aENST000003415173aENSE00001454221chr1:66378928-66379039112PDE4B_HUMAN1-14140--
1.4ENST000003415174ENSE00001314677chr1:66384280-66384518239PDE4B_HUMAN15-94800--
1.10cENST0000034151710cENSE00001295605chr1:66713143-66713337195PDE4B_HUMAN94-159660--
1.12ENST0000034151712ENSE00001648425chr1:66723330-6672336637PDE4B_HUMAN159-171130--
1.13ENST0000034151713ENSE00001301262chr1:66723476-6672354671PDE4B_HUMAN172-195240--
1.14aENST0000034151714aENSE00001328762chr1:66731721-6673177050PDE4B_HUMAN195-212180--
1.17eENST0000034151717eENSE00001765348chr1:66798191-66798303113PDE4B_HUMAN212-249380--
1.19bENST0000034151719bENSE00001321190chr1:66821210-6682130394PDE4B_HUMAN250-281320--
1.21ENST0000034151721ENSE00001308616chr1:66827298-66827476179PDE4B_HUMAN281-340602A:163-168
B:163-168
6
6
1.22eENST0000034151722eENSE00001292510chr1:66828851-6682894999PDE4B_HUMAN341-373332A:169-201
B:169-201
33
33
1.23bENST0000034151723bENSE00001311355chr1:66829090-66829254165PDE4B_HUMAN374-428552A:202-256
B:202-256
55
55
1.24ENST0000034151724ENSE00001294554chr1:66831350-66831449100PDE4B_HUMAN429-462342A:257-290
B:257-290
34
34
1.25bENST0000034151725bENSE00001326709chr1:66833379-66833533155PDE4B_HUMAN462-513522A:290-341
B:290-341
52
52
1.26aENST0000034151726aENSE00001304431chr1:66833626-66833748123PDE4B_HUMAN514-554412A:342-382
B:342-382
41
41
1.27ENST0000034151727ENSE00001597852chr1:66834470-66834652183PDE4B_HUMAN555-615612A:383-443
B:383-443
61
61
1.28cENST0000034151728cENSE00002180148chr1:66837996-668391871192PDE4B_HUMAN616-7361212A:444-485
B:444-485
42
42

(-) 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:323
 aligned with PDE4B_HUMAN | Q07343 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:323
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654   
          PDE4B_HUMAN   335 EDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIP 657
               SCOP domains d1xm4a_ A: Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xm4A00 A:163-485 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.21  Exon 1.22e  PDB: A:169-201       Exon 1.23b  PDB: A:202-256 UniProt: 374-428            Exon 1.24  PDB: A:257-290         ---------------------------------------------------Exon 1.26a  PDB: A:342-382               Exon 1.27  PDB: A:383-443 UniProt: 555-615                   Exon 1.28c  PDB: A:444-485 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------Exon 1.25b  PDB: A:290-341 UniProt: 462-513         ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1xm4 A 163 EDHLAKELEDLNKWGLNIFNVAGYSHNRPLTcIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMcDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIP 485
                                   172       182       192 |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482   
                                                         194-CME                                                                                                                                                                                                                                       432-CME                                                 

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with PDE4B_HUMAN | Q07343 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:323
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654   
          PDE4B_HUMAN   335 EDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIP 657
               SCOP domains d1xm4b_ B: Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xm4B00 B:163-485 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------------------------------------------------------------------PDEase_I-1xm4B01 B:233-477                                                                                                                                                                                                                           -------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------PDEase_I-1xm4B02 B:233-477                                                                                                                                                                                                                           -------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.21  Exon 1.22e  PDB: B:169-201       Exon 1.23b  PDB: B:202-256 UniProt: 374-428            Exon 1.24  PDB: B:257-290         ---------------------------------------------------Exon 1.26a  PDB: B:342-382               Exon 1.27  PDB: B:383-443 UniProt: 555-615                   Exon 1.28c  PDB: B:444-485 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------Exon 1.25b  PDB: B:290-341 UniProt: 462-513         ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1xm4 B 163 EDHLAKELEDLNKWGLNIFNVAGYSHNRPLTcIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHcDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIP 485
                                   172       182       192 |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482   
                                                         194-CME                                                                                                                       320-CME                                                                                                                                                                 

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDE4B_HUMAN | Q07343)
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:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0043015    gamma-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein gamma-tubulin.
    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:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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.
biological process
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    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:0035690    cellular response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071872    cellular response to epinephrine 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 an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:1901898    negative regulation of relaxation of cardiac muscle    Any process that stops, prevents or reduces the frequency, rate or extent of relaxation of cardiac muscle.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0001780    neutrophil homeostasis    The process of regulating the proliferation and elimination of neutrophils such that the total number of neutrophils within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032743    positive regulation of interleukin-2 production    Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
    GO:0086004    regulation of cardiac muscle cell contraction    Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
    GO:1901841    regulation of high voltage-gated calcium channel activity    Any process that modulates the frequency, rate or extent of high voltage-gated calcium channel activity.
    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:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    GO:0000930    gamma-tubulin complex    A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0005891    voltage-gated calcium channel complex    A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4B_HUMAN | Q073431f0j 1jp1 1jp2 1ro6 1ro9 1ror 1tb5 1xlx 1xlz 1xm6 1xmu 1xmy 1xn0 1xos 1xot 1y2h 1y2j 2chm 2qyl 3d3p 3frg 3g45 3gwt 3hc8 3hdz 3hmv 3kkt 3ly2 3o0j 3o56 3o57 3w5e 3wd9 4kp6 4myq 4nw7 4wzi 4x0f 5k6j

(-) Related Entries Specified in the PDB File

1xlx PDE4B IN COMPLEX WITH CILOMILAST
1xlz PDE4B IN COMPLEX WITH FILAMINAST
1xm6 PDE4B IN COMPLEX WITH (R)-MESOPRAM
1xmu PDE4B IN COMPLEX WITH ROFLUMILAST
1xmy PDE4B IN COMPLEX WITH (R)-ROLIPRAM
1xn0 PDE4B IN COMPLEX WITH (R,S)-ROLIPRAM
1xom PDE4D IN COMPLEX WITH CILOMILAST
1xon PDE4D IN COMPLEX WITH PICLAMILAST
1xoq PDE4D IN COMPLEX WITH ROFLUMILAST
1xor PDE4D IN COMPLEX WITH ZARDAVERINE
1xos PDE4B IN COMPLEX WITH SILDENAFIL
1xot PDE4B IN COMPLEX WITH VARDENAFIL
1xoz PDE5A IN COMPLEX WITH TADALAFIL
1xp0 PDE5A IN COMPLEX WITH VARDENAFIL