The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3db0 Target Id 380201
    Molecular Characteristics
    Source Listeria innocua clip11262
    Alias Ids TPS7236,NP_472219.1, Molecular Weight 14437.57 Da.
    Residues 127 Isoelectric Point 4.66
    Sequence meneledkilaileqhqvgvltsvqgdfpharymtflhdgltlytpsgkelpkteevrrnphvcvligy dspgsafleinglasleedesikeriweniskdwfqgedspsfvvikivpeqirilns
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.239
    Matthews' coefficent 2.07 Rfactor 0.182
    Waters 109 Solvent Content 40.44

    Ligand Information


    Google Scholar output for 3db0
    1. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
    2. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il

    Protein Summary

    NP_472219.1 is from LISTERIA INNOCUA.  It has sequence similarity to pyridoxine 5'-phosphate oxidases including Pyridoxine 5'-Phosphate Oxidase from Mycobacterium Tuberculosis (PDB code: 1xxo, sequence identity: 24%, BLAST E-value: 0.015) and Pyridoxine 5'-phoshate oxidase from Pseudomonas aeruginosa (PDB code: 1t9m, sequence identity: 14%, FFAS score: -37.500).  It also has sequence similarity to the Pyridox_oxidase (PF01243) family from Pfam (E-value: 1.7e-17).  Structurally, it is similar to proteins in the PNP-oxidase like family from SCOP, including
    a FMN-Binding protein from Desulfovibrio  vulgaris (PDB code: 1AXJ, 98 residues aligned with a RMSD of 2.2 A by SSM) and a FAD-binding protein (NP_107146.1) from Mesorhizobium loti (PDB code: 2HQ9, 99 residues aligned with a RMSD of 1.5 A by SSM), which was also solved by JCSG and also has a topsan page.  Interface interaction calculations suggest that the biomolecule of this protein may be a tetramer.

    Ligand Summary




    No references found.

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