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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH REGULATORY DOMAIN AND D155871
 
Authors :  B. L. Staker
Date :  03 Feb 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Phosphodiesterase, Pde4D, Ucr2, Alternative Splicing, Camp, Cytoplasm, Cytoskeleton, Hydrolase, Membrane, Metal- Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Burgin, O. T. Magnusson, J. Singh, P. Witte, B. L. Staker, J. M. Bjornsson, M. Thorsteinsdottir, S. Hrafnsdottir, T. Hagen, A. S. Kiselyov, L. J. Stewart, M. E. Gurney
Design Of Phosphodiesterase 4D (Pde4D) Allosteric Modulators For Enhancing Cognition With Improved Safety.
Nat. Biotechnol. V. 28 63 2010
PubMed-ID: 20037581  |  Reference-DOI: 10.1038/NBT.1598
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
    ChainsA, B, C, D
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentRESIDUES 299-347 AND 360-714
    GenePDE4D, DPDE3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDPDE3, PDE43

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2D714Ligand/Ion1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
3MG4Ligand/IonMAGNESIUM ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D711Ligand/Ion1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D711Ligand/Ion1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D711Ligand/Ion1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D711Ligand/Ion1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:50 , HIS A:330 , HIS A:366 , ASP A:367 , ASP A:484BINDING SITE FOR RESIDUE ZN A 801
02AC2SOFTWAREHOH A:80 , ASP A:367 , HOH A:586BINDING SITE FOR RESIDUE MG A 802
03AC3SOFTWAREHIS A:271BINDING SITE FOR RESIDUE CA A 4
04AC4SOFTWAREHOH A:54 , HOH A:154 , PHE A:196 , ILE A:197 , PHE A:201 , TYR A:325 , HIS A:326 , LEU A:485 , ASN A:487 , THR A:499 , ILE A:502 , MET A:503 , PHE A:506 , SER A:534 , GLN A:535 , PHE A:538BINDING SITE FOR RESIDUE D71 A 901
05AC5SOFTWAREHOH B:59 , HIS B:330 , HIS B:366 , ASP B:367 , ASP B:484BINDING SITE FOR RESIDUE ZN B 803
06AC6SOFTWAREHOH B:96 , HOH B:118 , ASP B:367 , HOH B:586BINDING SITE FOR RESIDUE MG B 804
07AC7SOFTWAREHOH B:82 , VAL B:193 , PHE B:196 , ILE B:197 , TYR B:325 , HIS B:326 , LEU B:485 , ASN B:487 , THR B:499 , ILE B:502 , PHE B:506 , SER B:534 , GLN B:535 , PHE B:538BINDING SITE FOR RESIDUE D71 B 902
08AC8SOFTWAREHOH C:34 , HIS C:330 , HIS C:366 , ASP C:367 , ASP C:484 , HOH C:587BINDING SITE FOR RESIDUE ZN C 805
09AC9SOFTWAREHOH C:72 , HOH C:88 , ASP C:367 , HOH C:587BINDING SITE FOR RESIDUE MG C 806
10BC1SOFTWAREHIS C:271 , ARG C:274BINDING SITE FOR RESIDUE CA C 2
11BC2SOFTWAREHOH C:31 , PHE C:196 , ILE C:197 , TYR C:325 , HIS C:326 , LEU C:485 , ASN C:487 , THR C:499 , ILE C:502 , PHE C:506 , MET C:523 , SER C:534 , GLN C:535 , PHE C:538 , HOH C:586BINDING SITE FOR RESIDUE D71 C 903
12BC3SOFTWAREHOH D:21 , HIS D:330 , HIS D:366 , ASP D:367 , ASP D:484BINDING SITE FOR RESIDUE ZN D 807
13BC4SOFTWAREHOH D:6 , HOH D:67 , HOH D:84 , HOH D:140 , ASP D:367BINDING SITE FOR RESIDUE MG D 808
14BC5SOFTWAREHIS D:271BINDING SITE FOR RESIDUE CA D 3
15BC6SOFTWAREHOH D:33 , VAL D:193 , PHE D:196 , ILE D:197 , TYR D:325 , HIS D:326 , LEU D:485 , ASN D:487 , THR D:499 , ILE D:502 , SER D:534 , GLN D:535 , PHE D:538BINDING SITE FOR RESIDUE D71 D 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G4G)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:555 -Pro A:556
2His B:555 -Pro B:556
3His C:555 -Pro C:556
4His D:555 -Pro D:556

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 20)

Asymmetric Unit (5, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069452V329APDE4D_HUMANDisease (ACRDYS2)  ---A/B/C/DV193A
2UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467A/B/C/DT451P
3UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---A/B/C/DE454A
4UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469A/B/C/DG537D
5UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188A/B/C/DI542T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069452V329APDE4D_HUMANDisease (ACRDYS2)  ---AV193A
2UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467AT451P
3UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---AE454A
4UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469AG537D
5UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188AI542T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069452V329APDE4D_HUMANDisease (ACRDYS2)  ---BV193A
2UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467BT451P
3UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---BE454A
4UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469BG537D
5UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188BI542T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069452V329APDE4D_HUMANDisease (ACRDYS2)  ---CV193A
2UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467CT451P
3UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---CE454A
4UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469CG537D
5UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188CI542T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069452V329APDE4D_HUMANDisease (ACRDYS2)  ---DV193A
2UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467DT451P
3UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---DE454A
4UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469DG537D
5UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188DI542T

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513
 
 
 
  4A:366-377
B:366-377
C:366-377
D:366-377
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513
 
 
 
  1A:366-377
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513
 
 
 
  1-
B:366-377
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513
 
 
 
  1-
-
C:366-377
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513
 
 
 
  1-
-
-
D:366-377

(-) Exons   (9, 36)

Asymmetric Unit (9, 36)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.13aENST0000034063513aENSE00001559328chr5:59189625-59188995631PDE4D_HUMAN1-1521520--
1.21bENST0000034063521bENSE00001136096chr5:58511794-58511603192PDE4D_HUMAN152-216650--
1.22ENST0000034063522ENSE00001682119chr5:58489362-5848932637PDE4D_HUMAN216-228130--
1.23ENST0000034063523ENSE00001754547chr5:58481088-5848101574PDE4D_HUMAN229-253250--
1.24ENST0000034063524ENSE00001719283chr5:58476470-5847642150PDE4D_HUMAN253-270180--
1.31dENST0000034063531dENSE00001750566chr5:58334798-58334686113PDE4D_HUMAN270-307380--
1.33bENST0000034063533bENSE00000914184chr5:58289292-5828919994PDE4D_HUMAN308-339324A:191-203
B:191-203
C:191-203
D:191-203
13
13
13
13
1.34ENST0000034063534ENSE00001136103chr5:58287831-58287659173PDE4D_HUMAN339-396584A:203-260 (gaps)
B:203-260 (gaps)
C:203-260 (gaps)
D:203-260 (gaps)
58
58
58
58
1.35ENST0000034063535ENSE00001001090chr5:58286729-5828663199PDE4D_HUMAN397-429334A:261-293
B:261-293
C:261-293
D:261-293
33
33
33
33
1.36ENST0000034063536ENSE00001001087chr5:58285746-58285582165PDE4D_HUMAN430-484554A:294-348
B:294-348
C:294-348
D:294-348
55
55
55
55
1.37ENST0000034063537ENSE00001001091chr5:58284419-58284320100PDE4D_HUMAN485-518344A:349-382
B:349-382
C:349-382
D:349-382
34
34
34
34
1.38ENST0000034063538ENSE00001175221chr5:58273172-58273018155PDE4D_HUMAN518-569524A:382-433
B:382-433
C:382-433
D:382-433
52
52
52
52
1.39ENST0000034063539ENSE00001001088chr5:58272299-58272177123PDE4D_HUMAN570-610414A:434-474
B:434-474
C:434-474
D:434-474
41
41
41
41
1.40ENST0000034063540ENSE00001698537chr5:58271666-58271484183PDE4D_HUMAN611-671614A:475-535
B:475-535
C:475-535
D:475-535
61
61
61
61
1.41jENST0000034063541jENSE00001989721chr5:58270907-582648656043PDE4D_HUMAN672-8091384A:536-579
B:536-578
C:536-580
D:536-578
44
43
45
43

(-) 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:338
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:389
                                   336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706         
          PDE4D_HUMAN   327 NQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQS 715
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..---------------------------------------------------.hhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33b   ---------------------------------------------------------Exon 1.35  PDB: A:261-293        Exon 1.36  PDB: A:294-348 UniProt: 430-484             Exon 1.37  PDB: A:349-382         ---------------------------------------------------Exon 1.39  PDB: A:434-474                Exon 1.40  PDB: A:475-535 UniProt: 611-671                   Exon 1.41j  PDB: A:536-579 UniProt: 672-809  Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.34  PDB: A:203-260 (gaps) UniProt: 339-396         -------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: A:382-433 UniProt: 518-569          -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3g4g A 191 NQVSEFISNTFLD---------------------------------------------------EDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQA 579
                                   200  |      -         -         -         -         -    |  260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570         
                                      203                                                 255                                                                                                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:388
                                   336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706        
          PDE4D_HUMAN   327 NQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 714
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..----------------------------------------------------hhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33b   ---------------------------------------------------------Exon 1.35  PDB: B:261-293        Exon 1.36  PDB: B:294-348 UniProt: 430-484             Exon 1.37  PDB: B:349-382         ---------------------------------------------------Exon 1.39  PDB: B:434-474                Exon 1.40  PDB: B:475-535 UniProt: 611-671                   Exon 1.41j  PDB: B:536-578 UniProt: 672-809 Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.34  PDB: B:203-260 (gaps) UniProt: 339-396         -------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: B:382-433 UniProt: 518-569          ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3g4g B 191 NQVSEFISNTFLD----------------------------------------------------DVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   200  |      -         -         -         -         -     | 260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570        
                                      203                                                  256                                                                                                                                                                                                                                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:339
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:390
                                   336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716
          PDE4D_HUMAN   327 NQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSP 716
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..---------------------------------------------------hhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T-------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33b   ---------------------------------------------------------Exon 1.35  PDB: C:261-293        Exon 1.36  PDB: C:294-348 UniProt: 430-484             Exon 1.37  PDB: C:349-382         ---------------------------------------------------Exon 1.39  PDB: C:434-474                Exon 1.40  PDB: C:475-535 UniProt: 611-671                   Exon 1.41j  PDB: C:536-580 UniProt: 672-809   Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.34  PDB: C:203-260 (gaps) UniProt: 339-396         -------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: C:382-433 UniProt: 518-569          --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3g4g C 191 NQVSEFISNTFLD---------------------------------------------------EDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAH 580
                                   200  |      -         -         -         -         -    |  260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
                                      203                                                 255                                                                                                                                                                                                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:337
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:388
                                   336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706        
          PDE4D_HUMAN   327 NQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 714
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.---------------------------------------------------hhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33b   ---------------------------------------------------------Exon 1.35  PDB: D:261-293        Exon 1.36  PDB: D:294-348 UniProt: 430-484             Exon 1.37  PDB: D:349-382         ---------------------------------------------------Exon 1.39  PDB: D:434-474                Exon 1.40  PDB: D:475-535 UniProt: 611-671                   Exon 1.41j  PDB: D:536-578 UniProt: 672-809 Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.34  PDB: D:203-260 (gaps) UniProt: 339-396         -------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: D:382-433 UniProt: 518-569          ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3g4g D 191 NQVSEFISNTFLD---------------------------------------------------EDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 578
                                   200  |      -         -         -         -         -    |  260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570        
                                      203                                                 255                                                                                                                                                                                                                                                                                                                                   

   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 3G4G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G4G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G4G)

(-) Gene Ontology  (52, 52)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PDE4D_HUMAN | Q08499)
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:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0031698    beta-2 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-2 adrenergic receptor.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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.
    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).
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
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:0071875    adrenergic receptor signaling pathway    A series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands.
    GO:0086024    adrenergic receptor signaling pathway involved in positive regulation of heart rate    An adrenergic receptor signaling pathway that contributes to an increase in frequency or rate of heart contraction. Binding of adrenalin or noradrenalin to a beta-adrenergic receptor on the surface of the signal-receiving cell results in the activation of an intracellular Gs protein. Gs activates adenylate cyclase to increase intracellular cyclic-AMP (cAMP) levels. cAMP binds directly to F-channels to allow an inward flow of sodium (known as funny current, or If current). The funny current is responsible for membrane depolarization and an increase in heart rate.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    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:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0071320    cellular response to cAMP    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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    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:0061028    establishment of endothelial barrier    The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0045822    negative regulation of heart contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    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: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:0032754    positive regulation of interleukin-5 production    Any process that activates or increases the frequency, rate, or extent of interleukin-5 production.
    GO:0030814    regulation of cAMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0086004    regulation of cardiac muscle cell contraction    Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
    GO:1901844    regulation of cell communication by electrical coupling involved in cardiac conduction    Any process that modulates the frequency, rate or extent of cell communication by electrical coupling involved in cardiac conduction.
    GO:0002027    regulation of heart rate    Any process that modulates the frequency or rate of heart contraction.
    GO:0010469    regulation of receptor activity    Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0010880    regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum    Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
    GO:0060314    regulation of ryanodine-sensitive calcium-release channel activity    Any process that modulates the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    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:0006939    smooth muscle contraction    A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0034704    calcium channel complex    An ion channel complex through which calcium ions pass.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    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
        PDE4D_HUMAN | Q084991e9k 1mkd 1oyn 1ptw 1q9m 1tb7 1tbb 1xom 1xon 1xoq 1xor 1y2b 1y2c 1y2d 1y2e 1y2k 1zkn 2fm0 2fm5 2pw3 2qyn 3g4i 3g4k 3g4l 3g58 3iad 3iak 3k4s 3sl3 3sl4 3sl5 3sl6 3sl8 3v9b 4ogb 4w1o 4wcu 5k1i 5k32 5tkb 5wqa

(-) Related Entries Specified in the PDB File

3g45 3g4i 3g4k 3g4l 3g58 3gpz