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The Open Protein Structure Annotation Network
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3d4r

    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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1760,NP_987166.1, 336099
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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



    References

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