The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of hypothetical protein (JCVI_PEP_1096665735785) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 2od4 Target Id 367439
    Molecular Characteristics
    Source Unknown
    Alias Ids TPS1509,JCVI_PEP_1096665735785 Molecular Weight 11464.61 Da.
    Residues 100 Isoelectric Point 6.57
    Sequence mfagsipmyirvvsitaqsklqfdmtvtyfenvwspkvislgaisaefvqsnensgmyiihypdkqtai svfdkikpevdevrtqnriqitegkrlfrvd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.193
    Matthews' coefficent 2.26 Rfactor 0.159
    Waters 188 Solvent Content 45.59

    Ligand Information


    Google Scholar output for 2od4
    1. Pfam 10 years on: 10 000 families and still growing
    SJ Sammut, RD Finn, A Bateman - Briefings in bioinformatics, 2008 - Oxford Univ Press
    2. Probing metagenomics by rapid cluster analysis of very large datasets
    W Li, JC Wooley, A Godzik - PLoS One, 2008 - dx.plos.org

    Protein Summary

    The gene ID JCVI_PEP_1096665735785 from a marine metagenome sample encodes a protein of unknown function.  

    The 2od4 structure belongs to the alpha+beta class, ferredoxin-like fold, dimeric alpha+beta barrel superfamily (SCOP54861).  However, no significant sequence similarity can be detected with known ferredoxin-like proteins. DALI top hits are with ferredoxin-like proteins such as 3e8o, 2fb0 and 1y0h (Z=11). Structurally, the protein is rather similar to the C-terminal domain of aminotransferase-like enzyme 3HT5.  Accordingly, a 26% sequence identity with the aminotransferase class I from Nitrosopumilus maritimus (YP_001581880) can be detected for the 28-90 fragment of this target.

    Ligand Summary





    No references found.

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