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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE8A CATALYTIC DOMAIN IN COMPLEX WITH IBMX
 
Authors :  H. Wang, Z. Yan, S. Yang, J. Cai, H. Robinson, H. Ke
Date :  01 Sep 08  (Deposition) - 25 Nov 08  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ibmx, Pde8A Catalytic Domain, Refolding, Alternative Splicing, Camp, Hydrolase, Magnesium, Manganese, Metal- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, Z. Yan, S. Yang, J. Cai, H. Robinson, H. Ke
Kinetic And Structural Studies Of Phosphodiesterase-8A And Implication On The Inhibitor Selectivity
Biochemistry V. 47 12760 2008
PubMed-ID: 18983167  |  Reference-DOI: 10.1021/BI801487X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIGH AFFINITY CAMP-SPECIFIC AND IBMX-INSENSITIVE 3',5'-CYCLIC PHOSPHODIESTERASE 8A
    ChainsA, B
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN OF PDE8A1 (UNP RESIDUES 482- 819)
    GenePDE8A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1IBM2Ligand/Ion3-ISOBUTYL-1-METHYLXANTHINE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IBM1Ligand/Ion3-ISOBUTYL-1-METHYLXANTHINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IBM1Ligand/Ion3-ISOBUTYL-1-METHYLXANTHINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:670 , ILE A:744 , TYR A:748 , PHE A:767 , GLN A:778 , PHE A:781 , PHE A:785 , HOH A:884BINDING SITE FOR RESIDUE IBM A 3
2AC2SOFTWAREHOH B:126 , MET B:670 , ILE B:744 , TYR B:748 , GLN B:778 , PHE B:781 , PHE B:785BINDING SITE FOR RESIDUE IBM B 3
3AC3SOFTWAREHIS A:560 , HIS A:596 , ASP A:597 , ASP A:726 , HOH A:820 , HOH A:821BINDING SITE FOR RESIDUE ZN A 1
4AC4SOFTWAREASP A:597 , HOH A:820 , HOH A:822 , HOH A:823 , HOH A:824 , HOH A:825BINDING SITE FOR RESIDUE MG A 2
5AC5SOFTWAREHOH B:11 , HOH B:12 , HIS B:560 , HIS B:596 , ASP B:597 , ASP B:726BINDING SITE FOR RESIDUE ZN B 1
6AC6SOFTWAREHOH B:11 , HOH B:13 , HOH B:14 , HOH B:15 , HOH B:16 , ASP B:597BINDING SITE FOR RESIDUE MG B 2

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:528 -A:533
2B:528 -B:533

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ECN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ECN)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE8A_HUMAN596-607
 
  2A:596-607
B:596-607
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE8A_HUMAN596-607
 
  1A:596-607
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE8A_HUMAN596-607
 
  1-
B:596-607

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003945532aENSE00001655579chr15:85525205-85525579375PDE8A_HUMAN1-62620--
1.3ENST000003945533ENSE00001764359chr15:85607601-8560765757PDE8A_HUMAN63-81190--
1.4ENST000003945534ENSE00001636622chr15:85610245-85610435191PDE8A_HUMAN82-145640--
1.5ENST000003945535ENSE00001618381chr15:85619093-8561914957PDE8A_HUMAN145-164200--
1.6ENST000003945536ENSE00001684152chr15:85619964-8562001855PDE8A_HUMAN164-182190--
1.7ENST000003945537ENSE00001755447chr15:85626787-8562687589PDE8A_HUMAN183-212300--
1.8ENST000003945538ENSE00001695435chr15:85632569-8563264779PDE8A_HUMAN212-238270--
1.10ENST0000039455310ENSE00001726628chr15:85634275-85634412138PDE8A_HUMAN239-284460--
1.11ENST0000039455311ENSE00001601720chr15:85641179-8564126789PDE8A_HUMAN285-314300--
1.12ENST0000039455312ENSE00001104439chr15:85643246-8564329752PDE8A_HUMAN314-331180--
1.13ENST0000039455313ENSE00001104423chr15:85643387-8564342943PDE8A_HUMAN332-346150--
1.14ENST0000039455314ENSE00001104415chr15:85652284-8565236178PDE8A_HUMAN346-372270--
1.15ENST0000039455315ENSE00001104468chr15:85656608-8565667871PDE8A_HUMAN372-395240--
1.16ENST0000039455316ENSE00001104402chr15:85657104-85657268165PDE8A_HUMAN396-450550--
1.17ENST0000039455317ENSE00001104405chr15:85658670-8565871849PDE8A_HUMAN451-467170--
1.18ENST0000039455318ENSE00001225334chr15:85659215-85659350136PDE8A_HUMAN467-512462A:482-512
B:482-512
31
31
1.19ENST0000039455319ENSE00001104432chr15:85660872-85661070199PDE8A_HUMAN512-578672A:512-578
B:512-578
67
67
1.20ENST0000039455320ENSE00001104459chr15:85664028-85664245218PDE8A_HUMAN579-651732A:579-651
B:579-651
73
73
1.21ENST0000039455321ENSE00001104456chr15:85666292-85666424133PDE8A_HUMAN651-695452A:651-695
B:651-695
45
45
1.22ENST0000039455322ENSE00001104435chr15:85669438-85669605168PDE8A_HUMAN696-751562A:696-751
B:696-751
56
56
1.23ENST0000039455323ENSE00001104452chr15:85679765-85679894130PDE8A_HUMAN752-795442A:752-795
B:752-795
44
44
1.24bENST0000039455324bENSE00001370034chr15:85681028-856823671340PDE8A_HUMAN795-829352A:795-819
B:795-819
25
25

(-) 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 PDE8A_HUMAN | O60658 from UniProtKB/Swiss-Prot  Length:829

    Alignment length:338
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811        
          PDE8A_HUMAN   482 DDVPPRIARAMENEEYWDFDIFELEAATHNRPLIYLGLKMFARFGICEFLHCSESTLRSWLQIIEANYHSSNPYHNSTHSADVLHATAYFLSKERIKETLDPIDEVAALIAATIHDVDHPGRTNSFLCNAGSELAILYNDTAVLESHHAALAFQLTTGDDKCNIFKNMERNDYRTLRQGIIDMVLATEMTKHFEHVNKFVNSINKPLATLEENGETDKNQEVINTMLRTPENRTLIKRMLIKCADVSNPCRPLQYCIEWAARISEEYFSQTDEEKQQGLPVVMPVFDRNTCSIPKSQISFIDYFITDMFDAWDAFVDLPDLMQHLDNNFKYWKGLDEM 819
               SCOP domains d3ecna_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: A:482-512      ------------------------------------------------------------------Exon 1.20  PDB: A:579-651 UniProt: 579-651                               --------------------------------------------Exon 1.22  PDB: A:696-751 UniProt: 696-751              Exon 1.23  PDB: A:752-795 UniProt: 752-795  ------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.19  PDB: A:512-578 UniProt: 512-578                         ------------------------------------------------------------------------Exon 1.21  PDB: A:651-695 UniProt: 651-695   ---------------------------------------------------------------------------------------------------Exon 1.24b  PDB: A:795-81 Transcript 1 (2)
                 3ecn A 482 DDVPPRIARAMENEEYWDFDIFELEAATHNRPLIYLGLKMFARFGICEFLHCSESTLRSWLQIIEANYHSSNPYHNSTHSADVLHATAYFLSKERIKETLDPIDEVAALIAATIHDVDHPGRTNSFLCNAGSELAILYNDTAVLESHHAALAFQLTTGDDKCNIFKNMERNDYRTLRQGIIDMVLATEMTKHFEHVNKFVNSINKPLATLEENGETDKNQEVINTMLRTPENRTLIKRMLIKCADVSNPCRPLQYCIEWAARISEEYFSQTDEEKQQGLPVVMPVFDRNTCSIPKSQISFIDYFITDMFDAWDAFVDLPDLMQHLDNNFKYWKGLDEM 819
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811        

Chain B from PDB  Type:PROTEIN  Length:338
 aligned with PDE8A_HUMAN | O60658 from UniProtKB/Swiss-Prot  Length:829

    Alignment length:338
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811        
          PDE8A_HUMAN   482 DDVPPRIARAMENEEYWDFDIFELEAATHNRPLIYLGLKMFARFGICEFLHCSESTLRSWLQIIEANYHSSNPYHNSTHSADVLHATAYFLSKERIKETLDPIDEVAALIAATIHDVDHPGRTNSFLCNAGSELAILYNDTAVLESHHAALAFQLTTGDDKCNIFKNMERNDYRTLRQGIIDMVLATEMTKHFEHVNKFVNSINKPLATLEENGETDKNQEVINTMLRTPENRTLIKRMLIKCADVSNPCRPLQYCIEWAARISEEYFSQTDEEKQQGLPVVMPVFDRNTCSIPKSQISFIDYFITDMFDAWDAFVDLPDLMQHLDNNFKYWKGLDEM 819
               SCOP domains d3ecnb_ B: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: B:482-512      ------------------------------------------------------------------Exon 1.20  PDB: B:579-651 UniProt: 579-651                               --------------------------------------------Exon 1.22  PDB: B:696-751 UniProt: 696-751              Exon 1.23  PDB: B:752-795 UniProt: 752-795  ------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.19  PDB: B:512-578 UniProt: 512-578                         ------------------------------------------------------------------------Exon 1.21  PDB: B:651-695 UniProt: 651-695   ---------------------------------------------------------------------------------------------------Exon 1.24b  PDB: B:795-81 Transcript 1 (2)
                 3ecn B 482 DDVPPRIARAMENEEYWDFDIFELEAATHNRPLIYLGLKMFARFGICEFLHCSESTLRSWLQIIEANYHSSNPYHNSTHSADVLHATAYFLSKERIKETLDPIDEVAALIAATIHDVDHPGRTNSFLCNAGSELAILYNDTAVLESHHAALAFQLTTGDDKCNIFKNMERNDYRTLRQGIIDMVLATEMTKHFEHVNKFVNSINKPLATLEENGETDKNQEVINTMLRTPENRTLIKRMLIKCADVSNPCRPLQYCIEWAARISEEYFSQTDEEKQQGLPVVMPVFDRNTCSIPKSQISFIDYFITDMFDAWDAFVDLPDLMQHLDNNFKYWKGLDEM 819
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDE8A_HUMAN | O60658)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0009187    cyclic nucleotide metabolic process    The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE8A_HUMAN | O606581lhq 1lxx 3ecm

(-) Related Entries Specified in the PDB File

3ecm