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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH VARDENAFIL
 
Authors :  W. Huanchen, Y. Mengchun, R. Howard, H. F. Sharron, K. Hengming
Date :  19 Oct 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cgmp Phosphodiesterase; Pde5-Inhibitor Potency; Vardenafil; Sildenafil; Levitratm. , Allosteric Enzyme, Alternative Splicing, Cgmp-Binding, Hydrolase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphorylation, Polymorphism, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, M. Ye, H. Robinson, S. H. Francis, H. Ke
Conformational Variations Of Both Phosphodiesterase-5 And Inhibitors Provide The Structural Basis For The Physiological Effects Of Vardenafil And Sildenafil.
Mol. Pharmacol. V. 73 104 2008
PubMed-ID: 17959709  |  Reference-DOI: 10.1124/MOL.107.040212
(for further references see the PDB file header)

(-) 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
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN OF PDE5A1: UNP RESIDUES 535- 860
    GenePDE5A, PDE5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE

 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
1VDN2Ligand/Ion2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1VDN1Ligand/Ion2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1VDN1Ligand/Ion2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:612 , HIS A:613 , CYS A:677 , ILE A:680 , ILE A:768 , ALA A:779 , MET A:816 , GLN A:817 , PHE A:820 , HOH A:865 , HOH A:894 , GLN B:854 , GLU B:858BINDING SITE FOR RESIDUE VDN A 1
2AC2SOFTWAREGLU A:858 , HOH A:976 , TYR B:612 , HIS B:613 , CYS B:677 , ILE B:680 , ILE B:768 , ALA B:779 , MET B:816 , GLN B:817 , PHE B:820 , HOH B:867 , HOH B:883BINDING SITE FOR RESIDUE VDN B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B2R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B2R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B2R)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  2A:653-660
B:653-659
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  1A:653-660
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE5A_HUMAN653-664
 
  1-
B:653-659

(-) 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:531-544
B:538-544
14
7
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:636-660
B:636-659
25
24
1.22ENST0000035496022ENSE00001016843chr4:120432289-12043220288PDE5A_HUMAN667-696302A:677-696
B:677-696
20
20
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:778-791
B:778-789
14
12
1.27aENST0000035496027aENSE00001016845chr4:120422408-12042232584PDE5A_HUMAN803-830282A:809-830
B:809-830
22
22
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:330
                                   540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860
          PDE5A_HUMAN   531 SAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
               SCOP domains d3b2ra_ A: cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3b2rA00 A:531-860 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......----------------hhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------PDEASE_I    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15b    Exon 1.18  PDB: A:545-593 UniProt: 545-593       Exon 1.19b  PDB: A:594-635                Exon 1.20c  PDB: A:636-660      -----------------------------Exon 1.23b  PDB: A:697-730        -------------------------Exon 1.25             Exon 1.26a  PDB: A:778-79Exon 1.27a  PDB: A:809-830  Exon 1.28c  PDB: A:831-860     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:677-696     ---------------------------------Exon 1.24b  PDB: A:730-756 -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3b2r A 531 GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGV----------------CHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGD-----------------KKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   540       550       560       570       580       590       600       610       620       630       640       650       660         -      |680       690       700       710       720       730       740       750       760       770       780       790|        -       810       820       830       840       850       860
                                                                                                                                                           660              677                                                                                                               791               809                                                   

Chain B from PDB  Type:PROTEIN  Length:287
 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 d3b2rb_ B: cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3b2rB00 B:538-860 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......-----------------.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------------------...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. 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:636-659      -----------------------------Exon 1.23b  PDB: B:697-730        -------------------------Exon 1.25             Exon 1.26a  PDB: B:778-78Exon 1.27a  PDB: B:809-830  Exon 1.28c  PDB: B:831-860     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: B:677-696     ---------------------------------Exon 1.24b  PDB: B:730-756 -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3b2r B 538 RELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRG-----------------CHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQ-------------------KKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   547       557       567       577       587       597       607       617       627       637       647       657 |       -       677       687       697       707       717       727       737       747       757       767       777       787 |       -         - |     817       827       837       847       857   
                                                                                                                                                   659               677                                                                                                             789                 809                                                   

   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  (0, 0)

(no "Pfam Domain" information available for 3B2R)

(-) 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 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3B2R)