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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS
 
Authors :  T. T. Chen, T. Chen, Y. C. Xu
Date :  17 Jun 11  (Deposition) - 24 Aug 11  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pde5A Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Xu, Z. Liu, T. Chen, T. T. Chen, Z. Wang, G. Tian, J. Shi, X. Wang, Y. Lu, X. Yan, G. Wang, H. Jiang, K. Chen, S. Wang, Y. Xu, J. Shen, W. Zhu
Utilization Of Halogen Bond In Lead Optimization: A Case Study Of Rational Design Of Potent Phosphodiesterase Type 5 (Pde5) Inhibitors.
J. Med. Chem. V. 54 5607 2011
PubMed-ID: 21714539  |  Reference-DOI: 10.1021/JM200644R

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
    ChainsA, B
    EC Number3.1.4.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 535-860
    GenePDE5, PDE5A
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPDE5A1, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB- PDE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15BO2Ligand/Ion5-BROMO-6-ETHYL-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15BO1Ligand/Ion5-BROMO-6-ETHYL-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15BO1Ligand/Ion5-BROMO-6-ETHYL-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:260 , HOH A:267 , TYR A:612 , ALA A:779 , PHE A:786 , LEU A:804 , MET A:816 , GLN A:817 , GLY A:819 , PHE A:820 , GLU B:858BINDING SITE FOR RESIDUE 5BO A 1
2AC2SOFTWAREGLU A:858 , HOH B:270 , TYR B:612 , MET B:816 , GLN B:817 , GLY B:819 , PHE B:820BINDING SITE FOR RESIDUE 5BO B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  2A:653-657
B:653-655
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  1A:653-657
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  1-
B:653-655

(-) Exons   (11, 22)

Asymmetric Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003549601aENSE00001851914chr4:120550146-120549675472PDE5A_HUMAN1-51510--
1.4ENST000003549604ENSE00001637089chr4:120528452-120527864589PDE5A_HUMAN51-2471970--
1.5bENST000003549605bENSE00000935544chr4:120517767-12051767890PDE5A_HUMAN248-277300--
1.6ENST000003549606ENSE00000970323chr4:120488299-12048822872PDE5A_HUMAN278-301240--
1.7ENST000003549607ENSE00000970324chr4:120486565-12048647690PDE5A_HUMAN302-331300--
1.8bENST000003549608bENSE00000970325chr4:120484125-120483988138PDE5A_HUMAN332-377460--
1.9ENST000003549609ENSE00000970326chr4:120481518-12048145168PDE5A_HUMAN378-400230--
1.10ENST0000035496010ENSE00000970327chr4:120474901-120474793109PDE5A_HUMAN400-436370--
1.11aENST0000035496011aENSE00000970328chr4:120473792-12047370588PDE5A_HUMAN437-466300--
1.13ENST0000035496013ENSE00000935541chr4:120463789-120463614176PDE5A_HUMAN466-524590--
1.15bENST0000035496015bENSE00000935545chr4:120460174-12046011560PDE5A_HUMAN525-544202A:538-544
B:537-544
7
8
1.18ENST0000035496018ENSE00001016848chr4:120446850-120446704147PDE5A_HUMAN545-593492A:545-593
B:545-593
49
49
1.19bENST0000035496019bENSE00001016844chr4:120442215-120442090126PDE5A_HUMAN594-635422A:594-635
B:594-635
42
42
1.20cENST0000035496020cENSE00001016846chr4:120440294-12044020095PDE5A_HUMAN636-667322A:636-657
B:636-655
22
20
1.22ENST0000035496022ENSE00001016843chr4:120432289-12043220288PDE5A_HUMAN667-696302A:680-696
B:680-696
17
17
1.23bENST0000035496023bENSE00001016840chr4:120428859-120428759101PDE5A_HUMAN697-730342A:697-730
B:697-730
34
34
1.24bENST0000035496024bENSE00001016847chr4:120427087-12042701078PDE5A_HUMAN730-756272A:730-756
B:730-756
27
27
1.25ENST0000035496025ENSE00001016842chr4:120425754-12042569164PDE5A_HUMAN756-777222A:756-777
B:756-777
22
22
1.26aENST0000035496026aENSE00001016841chr4:120423810-12042373675PDE5A_HUMAN778-802252A:778-802 (gaps)
B:778-802
25
25
1.27aENST0000035496027aENSE00001016845chr4:120422408-12042232584PDE5A_HUMAN803-830282A:803-830
B:803-830
28
28
1.28cENST0000035496028cENSE00001890486chr4:120419893-1204155504344PDE5A_HUMAN831-875452A:831-860
B:831-860
30
30

(-) 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:297
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:323
                                   547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857   
          PDE5A_HUMAN   538 RELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
               SCOP domains d3siea_ A: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....----------------------......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.15b  Exon 1.18  PDB: A:545-593 UniProt: 545-593       Exon 1.19b  PDB: A:594-635                Exon 1.20c  PDB: A:636-657      -----------------------------Exon 1.23b  PDB: A:697-730        -------------------------Exon 1.25             Exon 1.26a               Exon 1.27a  PDB: A:803-830  Exon 1.28c  PDB: A:831-860     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:680-696     ---------------------------------Exon 1.24b  PDB: A:730-756 -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3sie A 538 RELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDH----------------------IMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKE----PTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   547       557       567       577       587       597       607       617       627       637       647       657         -         -  |    687       697       707       717       727       737       747       757       767       777       787        |-   |   807       817       827       837       847       857   
                                                                                                                                                 657                    680                                                                                                                 796  801                                                           

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:324
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856    
          PDE5A_HUMAN   537 TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
               SCOP domains d3sieb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..------------------------......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.15b   Exon 1.18  PDB: B:545-593 UniProt: 545-593       Exon 1.19b  PDB: B:594-635                Exon 1.20c  PDB: B:636-655      -----------------------------Exon 1.23b  PDB: B:697-730        -------------------------Exon 1.25             Exon 1.26a  PDB: B:778-80Exon 1.27a  PDB: B:803-830  Exon 1.28c  PDB: B:831-860     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: B:680-696     ---------------------------------Exon 1.24b  PDB: B:730-756 -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3sie B 537 TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDL------------------------IMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   546       556       566       576       586       596       606       616       626       636       646        |-         -         -   |   686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856    
                                                                                                                                                655                      680                                                                                                                                                                                    

   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 3SIE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDE5A_HUMAN | O76074)
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:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside 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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0055118    negative regulation of cardiac muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    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:0060282    positive regulation of oocyte development    Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0030823    regulation of cGMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
    GO:0055119    relaxation of cardiac muscle    The process in which the extent of cardiac muscle contraction is reduced.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_HUMAN | O760741rkp 1t9r 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2chm 2h40 2h42 2h44 2xss 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

3shy 3shz