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 Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3d4r Target Id 381816
    Molecular Characteristics
    Source Methanococcus maripaludis s2
    Alias Ids TPS1760,NP_987166.1, 336099 Molecular Weight 17230.97 Da.
    Residues 150 Isoelectric Point 5.32
    Sequence mkipkiyvegelndgdrvaiekdgnaiiflekdeeysgngkllyqviyddlakymsldtlkkdvliqyp dkhtftylkagtklisvpaegykvypimdfgfrvlkgyrlatleskkgdlryvnspvsgtvifmneips eranyvfymlee
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.20 Rfree 0.236
    Matthews' coefficent 2.79 Rfactor 0.193
    Waters 532 Solvent Content 55.89

    Ligand Information


    Google Scholar output for 3d4r
    1. Assessment of CASP8 structure predictions for template free targets
    M Ben_David, O Noivirt_Brik, A Paz - Proteins: Structure, , 2009 - Wiley Online Library
    2. Analysis of CASP8 targets, predictions and assessment methods
    SY Shi, J Pei, RI Sadreyev, LN Kinch - Database: the journal , 2009 - ncbi.nlm.nih.gov
    3. FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular
    K Kanou, M Iwadate, T Hirata, G Terashi - Chemical & , 2009 - bioinf.jku.at
    4. The Fragment-based Consistency Score in Model Quality Assessment for De Novo Prediction of Protein Structures
    H Cetin, TN Sasaki, M Sasai - Chem-Bio Informatics Journal, 2011 - J-STAGE
    5. ___________________________________
    H Cetin_ _____ ____ - CBI _____, 2011 - J-STAGE
    6. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it

    Protein Summary

    The MMP0046 gene from Methanococcus maripaludis s2 encodes the NP_987166 protein belonging to the DUF2118 group (DUF2118, PF09891). It is also located in COG4072.  Genome context analysis provides a strong hit (0.88) with the bifunctional short chain isoprenyldiphosphate synthase, idsA (MMP0045).

    A DALI search with 3d4r as query only provides weak hits (Z-score=6) with the methylmalonyl-CoA decarboxylase gamma chain 2d5d and 1bdo.  


    Figure 1. Monomer form of 3d4r, colored blue (N-term) to red (C-term).

    Figure 2. Dimer of 3d4r.

    The monomer of 3d4r has some structural similarity to the inner lipoyl domain (L2) from the 60-meric transacetylase  core of pyruvate dehydrogenase complex (1y8p, Z=5), though the dimerization of 3d4r is distinct from how L2 interacts in its complex.

    Figure 3. 3d4r (blue) aligned with 1y8p (yellow).

    Ligand Summary





    No references found.

    Tag page

    Files (0)

    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch