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(-) Description

Title :  CRYSTAL STRUCTURE OF TBRPDEB1
 
Authors :  H. Wang, H. Ke
Date :  20 Nov 12  (Deposition) - 13 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Parasite Pde, Sleeping Sickness, African Trypanosomiasis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Jansen, H. Wang, A. J. Kooistra, C. De Graaf, K. M. Orrling, H. Tenor T. Seebeck, D. Bailey, I. J. De Esch, H. Ke, R. Leurs
Discovery Of Novel Trypanosoma Brucei Phosphodiesterase B1 Inhibitors By Virtual Screening Against The Unliganded Tbrpdeb1 Crystal Structure.
J. Med. Chem. V. 56 2087 2013
PubMed-ID: 23409953  |  Reference-DOI: 10.1021/JM3017877

(-) Compounds

Molecule 1 - CLASS 1 PHOSPHODIESTERASE PDEB1
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 576-918)
    Gene: PDEB1
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: PHOSPHODIESTERASE B1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:673 , HIS A:709 , ASP A:710 , ASP A:822 , HOH A:1101 , HOH A:1102BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:710 , HOH A:1101 , HOH A:1103 , HOH A:1104 , HOH A:1105 , HOH A:1106BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWAREHIS B:673 , HIS B:709 , ASP B:710 , ASP B:822 , HOH B:1101 , HOH B:1102BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREASP B:710 , HOH B:1101 , HOH B:1103 , HOH B:1104 , HOH B:1105 , HOH B:1106BINDING SITE FOR RESIDUE MG B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I15)

(-) Exons   (0, 0)

(no "Exon" information available for 4I15)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4i15a_ A: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i15 A 586 VTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIAYRLLLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIHTFLYRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILSSASGNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLATDMAKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDISRQWAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVAAPFFQKIVDACLQGMQWTVDRIKSNRAQWERVLETR 918
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915   


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4i15b_ B: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i15 B 586 VTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIAYRLLLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIHTFLYRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILSSASGNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLATDMAKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDISRQWAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVAAPFFQKIVDACLQGMQWTVDRIKSNRAQWERVLETR 918
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I15)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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