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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX WITH (R)-BAY73-6691
 
Authors :  H. Wang, X. Luo, M. Ye, J. Hou, H. Robinson, H. Ke
Date :  02 Oct 09  (Deposition) - 16 Feb 10  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Pde9, Catalytic Domain, Cgmp, Hydrolase, Manganese, Metal-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, X. Luo, M. Ye, J. Hou, H. Robinson, H. Ke
Insight Into Binding Of Phosphodiesterase-9A Selective Inhibitors By Crystal Structures And Mutagenesis
J. Med. Chem. V. 53 1726 2010
PubMed-ID: 20121115  |  Reference-DOI: 10.1021/JM901519F

(-) Compounds

Molecule 1 - HIGH AFFINITY CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 9A
    ChainsA, B
    EC Number3.1.4.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePDE9A, PDE9A2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PDB2Ligand/Ion1-(2-CHLOROPHENYL)-6-[(2R)-3,3,3-TRIFLUORO-2-METHYLPROPYL]-1,7-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PDB2Ligand/Ion1-(2-CHLOROPHENYL)-6-[(2R)-3,3,3-TRIFLUORO-2-METHYLPROPYL]-1,7-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PDB2Ligand/Ion1-(2-CHLOROPHENYL)-6-[(2R)-3,3,3-TRIFLUORO-2-METHYLPROPYL]-1,7-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:256 , HIS A:292 , ASP A:293 , ASP A:402 , HOH A:701 , HOH A:702BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREASP A:293 , HOH A:702 , HOH A:703 , HOH A:704 , HOH A:705 , HOH A:706BINDING SITE FOR RESIDUE MG A 602
3AC3SOFTWAREHIS A:252 , VAL A:417 , LEU A:420 , LEU A:421 , TYR A:424 , ALA A:452 , GLN A:453 , PHE A:456 , HOH A:709BINDING SITE FOR RESIDUE PDB A 600
4AC4SOFTWAREHIS B:256 , HIS B:292 , ASP B:293 , ASP B:402 , MG B:602 , HOH B:711BINDING SITE FOR RESIDUE ZN B 601
5AC5SOFTWAREASP B:293 , ZN B:601 , HOH B:712 , HOH B:713 , HOH B:714 , HOH B:715BINDING SITE FOR RESIDUE MG B 602
6AC6SOFTWAREHIS B:252 , LEU B:420 , LEU B:421 , TYR B:424 , ALA B:452 , GLN B:453 , PHE B:456BINDING SITE FOR RESIDUE PDB B 600

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:241 -B:338

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K3E)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE9A_HUMAN352-363
 
  2A:292-303
B:292-303
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE9A_HUMAN352-363
 
  2A:292-303
B:292-303
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE9A_HUMAN352-363
 
  2A:292-303
B:292-303

(-) Exons   (10, 20)

Asymmetric Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000002915391dENSE00002151102chr21:44073865-44073993129PDE9A_HUMAN1-23230--
1.2aENST000002915392aENSE00001050441chr21:44106302-4410637271PDE9A_HUMAN24-47240--
1.3ENST000002915393ENSE00001747303chr21:44108027-4410810478PDE9A_HUMAN47-73270--
1.5bENST000002915395bENSE00001592516chr21:44119078-4411912144PDE9A_HUMAN73-88160--
1.8bENST000002915398bENSE00001792262chr21:44151880-44152059180PDE9A_HUMAN88-148610--
1.9ENST000002915399ENSE00001050439chr21:44152180-4415223455PDE9A_HUMAN148-166190--
1.10ENST0000029153910ENSE00001050446chr21:44153466-4415353671PDE9A_HUMAN166-190250--
1.11ENST0000029153911ENSE00001050442chr21:44163886-4416397085PDE9A_HUMAN190-218290--
1.12ENST0000029153912ENSE00001292678chr21:44171226-4417130782PDE9A_HUMAN218-245280--
1.13ENST0000029153913ENSE00001050443chr21:44174100-4417417475PDE9A_HUMAN246-270252A:187-210
B:187-210
24
24
1.14bENST0000029153914bENSE00001050445chr21:44179109-4417919587PDE9A_HUMAN271-299292A:211-239
B:211-239
29
29
1.15ENST0000029153915ENSE00001050438chr21:44180438-44180542105PDE9A_HUMAN300-334352A:240-274
B:240-274
35
35
1.16ENST0000029153916ENSE00001050435chr21:44180935-4418101783PDE9A_HUMAN335-362282A:275-302
B:275-302
28
28
1.17bENST0000029153917bENSE00001050447chr21:44182193-44182349157PDE9A_HUMAN362-414532A:302-354
B:302-354
53
53
1.18ENST0000029153918ENSE00001050433chr21:44185491-44185604114PDE9A_HUMAN415-452382A:355-392
B:355-392
38
38
1.19aENST0000029153919aENSE00001050450chr21:44188298-44188402105PDE9A_HUMAN453-487352A:393-427
B:393-427
35
35
1.20ENST0000029153920ENSE00001050437chr21:44189137-44189265129PDE9A_HUMAN488-530432A:428-470
B:428-470
43
43
1.21ENST0000029153921ENSE00001309081chr21:44190813-4419090896PDE9A_HUMAN531-562322A:471-502
B:471-502
32
32
1.22ENST0000029153922ENSE00001050432chr21:44192549-4419263082PDE9A_HUMAN563-590282A:503-506
B:503-506
4
4
1.23ENST0000029153923ENSE00001851903chr21:44195390-44195619230PDE9A_HUMAN590-59340--

(-) 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:320
 aligned with PDE9A_HUMAN | O76083 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:320
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566
          PDE9A_HUMAN   247 LLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 566
               SCOP domains d3k3ea_ A: High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3k3eA00 A:187-506 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------PDEASE_I    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13  PDB: A:187-21Exon 1.14b  PDB: A:211-239   Exon 1.15  PDB: A:240-274          Exon 1.16  PDB: A:275-302   ----------------------------------------------------Exon 1.18  PDB: A:355-392             Exon 1.19a  PDB: A:393-427         Exon 1.20  PDB: A:428-470 UniProt: 488-530 Exon 1.21  PDB: A:471-502       1.22 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.17b  PDB: A:302-354 UniProt: 362-414          -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3k3e A 187 LLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 506
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with PDE9A_HUMAN | O76083 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:320
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566
          PDE9A_HUMAN   247 LLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 566
               SCOP domains d3k3eb_ B: High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3k3eB00 B:187-506 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ----------------------------------------------------------------PDEase_I-3k3eB01 B:251-487                                                                                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------PDEase_I-3k3eB02 B:251-487                                                                                                                                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------PDEASE_I    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13  PDB: B:187-21Exon 1.14b  PDB: B:211-239   Exon 1.15  PDB: B:240-274          Exon 1.16  PDB: B:275-302   ----------------------------------------------------Exon 1.18  PDB: B:355-392             Exon 1.19a  PDB: B:393-427         Exon 1.20  PDB: B:428-470 UniProt: 488-530 Exon 1.21  PDB: B:471-502       1.22 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.17b  PDB: B:302-354 UniProt: 362-414          -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3k3e B 187 LLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKK 506
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506

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

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDE9A_HUMAN | O76083)
molecular function
    GO:0047555    3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0046068    cGMP metabolic process    The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate.
    GO:0019934    cGMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE9A_HUMAN | O760832hd1 2yy2 3dy8 3dyl 3dyn 3dyq 3dys 3jsi 3jsw 3k3h 3n3z 3qi3 3qi4 4e90 4g2j 4g2l 4gh6 4y86 4y87 4y8c

(-) Related Entries Specified in the PDB File

3k3h CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX WITH (S)-BAY73-6691