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The Open Protein Structure Annotation Network
PDB Keyword
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3ceb

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

    Title Crystal structure of D-aminoacid Aminotransferase-Like PLP-Dependent Enzyme (YP_718332.1) from Haemophilus somnus 129PT at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 3ceb Target Id 377935
    Molecular Characteristics
    Source Haemophilus somnus 129pt
    Alias Ids TPS1701,YP_718332.1, _0017.002340_ Molecular Weight 23161.79 Da.
    Residues 193 Isoelectric Point 8.88
    Sequence mwqfplfetilieqgqaknisyhqqryeksllkfypkmklqpfdlakiiakhtalfthreglircridy nhhdyvlqcfpyqqkvyrtfkpvfcdhidyslkfsdrtllnnllkqkeecdeimiirqgkvtdcsignl ifrqnnqwitpdkpllegtqraklleqkkiiareiffedlaqyeeirlinamngl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.225
    Matthews' coefficent 4.65 Rfactor 0.186
    Waters 85 Solvent Content 73.57

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ceb
    1. PURIFICATION OF LYSINE DECARBOXYLASE: A MODEL SYSTEM FOR PLP ENZYME INHIBITOR DEVELOPMENT AND STUDY
    LC Zohner - 2011 - digitalcommons.unl.edu
     

    Protein Summary

    Gene HS_0128 from Haemophilus somnus 129pt translates into the YP_718332 amino acid sequence, which has sequence similarity to those in the amino transferase class 4 group ( aminotran_4 (PF01063) family ) ( FFAS score: -46.500). Analysis of HS_0128 genome context indicates the presence of an amino deoxychorismate synthase subunit I (pabB, HS_0129) as putative functional partner.

    3ceb belongs in the D-aminoacid aminotransferase-like PLP-dependent enzymes (super)family from SCOP. DALI top hit are with the 4-amino 4-deoxy chorismate lyase PDB:3lul (Z=18), 4-amino-4-deoxychorismate lyase PDB:1et0; Z=17), or the d-amino acid aminotransferase (PDB:1daa; Z=17).  3ceb consists of two domains (1-82 and 83-203). The biomolecule of this target should be a monomer based on interface interaction calculation. A pyridoxyal-5'-phosphate (PLP) molecule has been built in current model covalently bound to Lys 102, which is in a pocket of the C-terminal domain around the domain interface.

    3ceb consists of two domains: N-terminal domain (Magentas: 1 -82) and C-terminal domain (Green: 83-293). One PLP molecule is found covalently bonded to Lys 102 from the C-terminal domain.

    Ligand Summary

    Ligands: LYSINE PYRIDOXAL-5'-PHOSPHATE 


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