Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH BOUND ALLOSTERIC MODULATOR
 
Authors :  B. L. Staker, A. B. Burgin Jr.
Date :  13 Jul 09  (Deposition) - 05 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
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 :  Pde4D, Allosteric Modulatory, Inhibitor, 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 SystemUNIDENTIFIED BACULOVIRUS
    Expression System PlasmidPBACGUS
    Expression System Taxid10469
    Expression System Vector TypePLASMID
    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, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
115X4Ligand/Ion1-{4-[(2-FLUORO-6-METHOXY-3'-NITROBIPHENYL-3-YL)METHYL]PHENYL}UREA
2EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG4Ligand/IonMAGNESIUM ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
115X1Ligand/Ion1-{4-[(2-FLUORO-6-METHOXY-3'-NITROBIPHENYL-3-YL)METHYL]PHENYL}UREA
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
115X1Ligand/Ion1-{4-[(2-FLUORO-6-METHOXY-3'-NITROBIPHENYL-3-YL)METHYL]PHENYL}UREA
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
115X1Ligand/Ion1-{4-[(2-FLUORO-6-METHOXY-3'-NITROBIPHENYL-3-YL)METHYL]PHENYL}UREA
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
115X1Ligand/Ion1-{4-[(2-FLUORO-6-METHOXY-3'-NITROBIPHENYL-3-YL)METHYL]PHENYL}UREA
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:34 , HIS A:326 , SER A:374 , LEU A:485 , ILE A:502 , SER A:534 , GLN A:535 , PHE A:538 , PHE A:599 , THR A:603BINDING SITE FOR RESIDUE 15X A 901
02AC2SOFTWAREHOH A:178 , HIS A:330 , HIS A:366 , ASP A:367 , ASP A:484BINDING SITE FOR RESIDUE ZN A 620
03AC3SOFTWAREHOH A:178 , HOH A:190 , ASP A:367BINDING SITE FOR RESIDUE MG A 621
04AC4SOFTWAREHIS A:271 , VAL A:272 , PHE A:273 , ARG A:274 , GLU A:277 , LEU A:494 , GLN A:497BINDING SITE FOR RESIDUE EPE A 806
05AC5SOFTWAREHOH B:31 , HOH B:73 , HOH B:163 , HIS B:326 , HIS B:370 , VAL B:373 , SER B:374 , LEU B:485 , ILE B:502 , PHE B:506 , SER B:534 , GLN B:535 , PHE B:538 , PHE B:599 , THR B:603 , PHE B:604BINDING SITE FOR RESIDUE 15X B 901
06AC6SOFTWAREHOH B:180 , HOH B:195 , HIS B:330 , HIS B:366 , ASP B:367 , ASP B:484BINDING SITE FOR RESIDUE ZN B 620
07AC7SOFTWAREHOH B:31 , HOH B:170 , HOH B:180 , HOH B:181 , ASP B:367 , GLU B:396BINDING SITE FOR RESIDUE MG B 621
08AC8SOFTWAREHOH B:112 , ASP B:306 , THR B:307 , ASN B:411 , GLN B:416 , LYS B:456 , LYS B:457 , THR C:419 , LYS C:420BINDING SITE FOR RESIDUE EPE B 801
09AC9SOFTWAREHIS B:271 , VAL B:272 , PHE B:273 , ARG B:274 , GLU B:277 , GLN B:493 , GLN B:497BINDING SITE FOR RESIDUE EPE B 802
10BC1SOFTWAREHIS C:326 , HIS C:370 , VAL C:373 , SER C:374 , LEU C:485 , ILE C:502 , SER C:534 , GLN C:535 , PHE C:538 , PHE C:599 , PHE C:604BINDING SITE FOR RESIDUE 15X C 901
11BC2SOFTWAREHOH C:182 , HOH C:186 , HIS C:330 , HIS C:366 , ASP C:367 , ASP C:484BINDING SITE FOR RESIDUE ZN C 620
12BC3SOFTWAREHOH C:182 , HOH C:183 , HOH C:184 , HOH C:185 , ASP C:367BINDING SITE FOR RESIDUE MG C 621
13BC4SOFTWAREHIS C:271 , VAL C:272 , PHE C:273 , ARG C:274 , GLU C:277 , GLN C:493 , LEU C:494 , GLN C:497BINDING SITE FOR RESIDUE EPE C 803
14BC5SOFTWAREHOH D:203 , HIS D:326 , HIS D:370 , VAL D:373 , SER D:374 , LEU D:485 , THR D:499 , ILE D:502 , MET D:523 , SER D:534 , GLN D:535 , PHE D:538 , PHE D:599BINDING SITE FOR RESIDUE 15X D 901
15BC6SOFTWAREHOH D:179 , HOH D:196 , HIS D:330 , HIS D:366 , ASP D:367 , ASP D:484BINDING SITE FOR RESIDUE ZN D 620
16BC7SOFTWAREHOH D:179 , HOH D:189 , HOH D:192 , HOH D:197 , HOH D:203 , ASP D:367BINDING SITE FOR RESIDUE MG D 621
17BC8SOFTWAREGLU D:261 , ASP D:264 , TRP D:268 , HIS D:271BINDING SITE FOR RESIDUE EPE D 804
18BC9SOFTWAREHIS D:271 , PHE D:273 , ARG D:274 , GLU D:277 , GLN D:493 , LEU D:494 , GLN D:497BINDING SITE FOR RESIDUE EPE D 805

(-) SS Bonds  (0, 0)

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

(-) 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  (4, 16)

Asymmetric Unit (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467A/B/C/DT451P
2UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---A/B/C/DE454A
3UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469A/B/C/DG537D
4UniProtVAR_069455I678TPDE4D_HUMANDisease (ACRDYS2)587777188A/B/C/DI542T

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

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

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

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068245T587PPDE4D_HUMANDisease (ACRDYS2)397514467DT451P
2UniProtVAR_069453E590APDE4D_HUMANDisease (ACRDYS2)  ---DE454A
3UniProtVAR_069454G673DPDE4D_HUMANDisease (ACRDYS2)397514469DG537D
4UniProtVAR_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   (8, 32)

Asymmetric Unit (8, 32)
 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_HUMAN308-339320--
1.34ENST0000034063534ENSE00001136103chr5:58287831-58287659173PDE4D_HUMAN339-396584A:249-260
B:254-260
C:252-260
D:254-260
12
7
9
7
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:536-606 (gaps)
B:536-606 (gaps)
C:536-606 (gaps)
D:536-606 (gaps)
71
71
110
110

(-) 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:340
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:357
                                   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       664       674       684       694       704       714       724       734       
          PDE4D_HUMAN   385 GVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLE 741
               SCOP domains d3iada_ A: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.-----------------hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.34   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:536-606 (gaps) UniProt: 672-809 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: A:382-433 UniProt: 518-569          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iad A 249 GVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQST-----------------NQVSEFISNTFLD 606
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568      |  -         -    |  599       
                                                                                                                                                                                                                                                                                                                                                                575               594            

Chain B from PDB  Type:PROTEIN  Length:338
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:352
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739  
          PDE4D_HUMAN   390 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLE 741
               SCOP domains d3iadb_ B: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..--------------hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.34   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:536-606 (gaps) UniProt: 672-809 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: B:382-433 UniProt: 518-569          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iad B 254 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ--------------NQVSEFISNTFLD 606
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573    |    -       594       604  
                                                                                                                                                                                                                                                                                                                                                              578            594            

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

    Alignment length:394
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777    
          PDE4D_HUMAN   388 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLEEDGESDTEKDSGSQVEEDTSCSDSKTLCTQDSESTEIPLD 781
               SCOP domains d3iadc_ C: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..----------------------------------------.hhhhhhhhhh---------------hh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.34Exon 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:536-606 (gaps) UniProt: 672-809 [INCOMPLETE]                                                Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: C:382-433 UniProt: 518-569          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iad C 252 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTI----------------------------------------GNQVSEFISNT---------------FLD 606
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571    |    -         -         -         -     | 597     |   -         - |  
                                                                                                                                                                                                                                                                                                                                                              576                                      593       603             604  

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

    Alignment length:392
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779  
          PDE4D_HUMAN   390 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLEEDGESDTEKDSGSQVEEDTSCSDSKTLCTQDSESTEIPLD 781
               SCOP domains d3iadd_ D: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....--------------------------------------.hhhhhhhhhh---------------hh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.34   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:536-606 (gaps) UniProt: 672-809 [INCOMPLETE]                                                Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: D:382-433 UniProt: 518-569          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iad D 254 QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ--------------------------------------GNQVSEFISNT---------------FLD 606
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573    |    -         -         -         -   |   599   |     -       604  
                                                                                                                                                                                                                                                                                                                                                              578                                    593       603             604  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    15X  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:555 - Pro A:556   [ RasMol ]  
    His B:555 - Pro B:556   [ RasMol ]  
    His C:555 - Pro C:556   [ RasMol ]  
    His D:555 - Pro D:556   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) 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
  3iad
    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
  PDE4D_HUMAN | Q08499
    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)
  614613
    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
  PDE4D_HUMAN | Q08499
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 3g4g 3g4i 3g4k 3g4l 3g58 3iak 3k4s 3sl3 3sl4 3sl5 3sl6 3sl8 3v9b 4ogb 4w1o 4wcu 5k1i 5k32 5tkb 5wqa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3IAD)