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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH INHIBITOR 5R
 
Authors :  W. Cui, M. Huang, Y. Shao, H. Luo
Date :  22 Aug 13  (Deposition) - 09 Jul 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Inhibitor Complex, Phosphodiesterase, Pde5 Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. N. Shang, Y. X. Shao, Y. H. Cai, M. Guan, M. Huang, W. Cui, L. He, Y. J. Yu L. Huang, Z. Li, X. Z. Bu, H. Ke, H. B. Luo
Discovery Of 3-(4-Hydroxybenzyl)-1-(Thiophen-2-Yl)Chromeno[2, 3-C]Pyrrol- 9(2H)-One As A Phosphodiesterase-5 Inhibitor And Its Comple Crystal Structure.
Biochem Pharmacol V. 89 86 2014
PubMed-ID: 24565909  |  Reference-DOI: 10.1016/J.BCP.2014.02.013

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 535-860)
    Gene: PDE5A, PDE5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB-PDE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
124E1Ligand/Ion3-(4-HYDROXYBENZYL)-1-(THIOPHEN-2-YL)CHROMENO[2,3-C]PYRROL-9(2H)-ONE
2MG1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:613 , HIS A:617 , ASP A:654 , ASP A:764 , 24E A:902 , ZN A:903 , HOH A:1002BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWARELEU A:725 , ALA A:767 , ILE A:768 , GLN A:775 , VAL A:782 , ALA A:783 , PHE A:787 , ILE A:813 , MET A:816 , GLN A:817 , PHE A:820 , SO4 A:901BINDING SITE FOR RESIDUE 24E A 902
3AC3SOFTWAREHIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , SO4 A:901 , MG A:904 , HOH A:1001BINDING SITE FOR RESIDUE ZN A 903
4AC4SOFTWAREASP A:654 , ZN A:903 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1004 , HOH A:1005BINDING SITE FOR RESIDUE MG A 904

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:677 -A:677

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MD6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MD6)

(-) Exons   (0, 0)

(no "Exon" information available for 4MD6)

(-) Sequences/Alignments

Asymmetric/Biological 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4md6 A 535 EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGEKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ 860
                                   544       554       564       574       584       594       604       614       624       634       644       654       664 ||    684       694       704       714       724       734       744       754       764       774       784     ||811       821       831       841       851         
                                                                                                                                                             666|                                                                                                              790|                                                    
                                                                                                                                                              677                                                                                                               808
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MD6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MD6)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_HUMAN | O76074: 1rkp 1t9r 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2chm 2h40 2h42 2h44 2xss 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4oew 4oex 5jo3

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