.
The Open Protein Structure Annotation Network
PDB Keyword
.

3ddj

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

    Title Crystal structure of CBS domain-containing protein in complex with AMP (NP_344512.1) from SULFOLOBUS SOLFATARICUS at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3ddj Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS7232,NP_344512.1, 283043
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 1
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.32 Rfactor 0.168
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 46.97

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3ddj
    1. Crystal Structures of the CBS and DRTGG Domains of the Regulatory Region of Clostridium perfringens Pyrophosphatase Complexed with the Inhibitor
    H Tuominen, A Salminen, E Oksanen, J Jmsen - Journal of molecular , 2010 - Elsevier
     
    2. Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human
    R Lahti, J Jmsen, H Tuominen, AA Baykov - 2011 - tara.tcd.ie
     
    3. The CBS Domain: A Protein Module with an Emerging Prominent Role in Regulation
    AA Baykov, HK Tuominen, R Lahti - ACS Chemical Biology, 2011 - ACS Publications
     
    4. An integrated database for complex protein structure modeling
    Q Wang, RL Dunbrack - Bioinformatics and Biomeidcine , 2008 - ieeexplore.ieee.org
     
    5. THE STruCTurAL BASiS For iNorGANiC PyroPHoSPHATASE CATALySiS AND rEGuLATioN
    H Tuominen - 2011 - doria.fi
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Gene SSO3205 from Sulfolobus solfataricus encodes the NP_344512 protein containing 4 CBS domains (PF00571).

    SCOP classifies 3ddj in the alpha_beta class, CBS-domain pair (super)family. According to DALI, 3ddj is structurally highly similar to

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    , the human AMP activated kinase gamma-1 subunit despite low sequence similarity (rmsd 2.1A for 228 aligned Ca; 16% seq id; Z=24). Other related homologs are
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    /
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    /
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    /
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    and
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    /
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    .

    3ddj fold consists of two CBS domain pairs forming a ring. However, it only contains 1 AMP molecule bound while the AMPK gamma structure shows multiple nucleotides bound. The AMP site appears to be able to bind ATP as well. It  is not clear whether other binding sites in 3ddj can interact with AMP/ADP/ATP. Potentially important residues include the highly conserved residues with numbers according to PDB 44,50, 80,100, 104-112, 119-124, 143,163, 168-173, 182-186, 230,231,234, 240,242, 253-260.


    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    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