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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution. To be published
    Site JCSG
    PDB Id 3pgv Target Id 388334
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS7512,YP_001337957.1, 60679758, 91403 Molecular Weight 30083.58 Da.
    Residues 266 Isoelectric Point 5.27
    Sequence myqvvasdldgtllspdhfltpyaketlklltarginfvfatgrhyidvgqirdnlgirsymitsngar vhdsdgqqifahnldrdiaadlfeivrndpkivtnvyredewymnrhrpeemrffkeavfnyklyepge ldpqgiskvfftcedhehllpleqamnarwgdrvnvsfstltclevmaggvskghaleavakmlgytls dciafgdgmndaemlsmagkgcimanahqrlkdlhpelevigsnaddavprylrklyld
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.39 Rfree 0.2106
    Matthews' coefficent 2.35 Rfactor 0.1666
    Waters 428 Solvent Content 47.68

    Ligand Information


    Google Scholar output for 3pgv

    Protein Summary

     Target ID 388344 belongs to the Hydrolase_3 (PF08282) Pfam family. The Pfam family include members of the haloacid-dehalogenase-like hydrolases (HAD), a diverse group of enzymes The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification (see [Ref], [Ref], [Ref] for reviews).



    Shown to the right is a ribbons representation of the structure of target ID 388344 with the N-terminal region in blue and the C-terminal region in red. Shown as a grey sphere is a magnesium atom modeled into the structure. The modeling of magnesium is supported by the presence of a similarly-bound magnesium in related structures. A molecule of HEPES from the crystallization buffer was also modeled into the structure and is shown by a stick representation.





    A DALI search shows that the structure of target ID 388344 reported here is similar to the following structures:

    PDB ID
    DALI Z-Score
    rmsd overlap (Ang)
    number of aligned residues
    % sequence ID
    Hit Contains Mg?
    1rkq_A 31.4 2.2 252/271 29 Crystal structure of HAD-like phosphatase yidA from E. coli New York Structural Genomics Research Consortium  
    1nrw_A 31.1 2.3 252/285 27 The structure of a HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. SUBTILIS Midwest Center for Structural Genomics  
    3dnp_A 30.1 2.5 250/275 22

    Crystal structure of Stress response protein yhaX from Bacillus subtilis

    Midwest Center for Structural Genomics  
    1rlo_D  29.7 2.1 246/268 20 Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12  [Ref]  
    1rlm_A 29.3 2.3 249/269 20 Crystal Structure of ybiV from Escherichia coli K12  [Ref]  
    1ymq_A 29.1 2.2 244/260 18 HAD Superfamily Phosphotransferase Substrate Diversification: Structure and Function Analysis of the HAD Subclass IIB Sugar Phosphatase BT4131   [Ref]  
    1rlt_C 28.9 2.3 246/268 28 Transition State Analogue of ybiV from E. coli K12  [Ref]  
    2rb5_A 28.9 2,3 245/261 18 X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.  [Ref]  








    Ligand Summary

    Pfam:  This one belongs to Pfam family Hydrolase_3




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