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The Open Protein Structure Annotation Network
PDB Keyword
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1vkd

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

    Title Crystal structure of hypothetical protein (TM1225) from Thermotoga maritima at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 1vkd Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1270,TM1225, _0065.000420_, 84757
    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 2.36 Rfactor 0.16203
    Waters
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    Solvent Content 47.48

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 1vkd
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
     
    3. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    4. Structure-based design of an urokinase-type plasminogen activator receptorderived peptide inhibiting cell migration and lung metastasis
    MV Carriero, I Longanesi-Cattani, K Bifulco - Molecular cancer , 2009 - AACR
     
    5. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions
    D McMullan, JM Canaves, K Quijano - Journal of structural and , 2005 - Springer
     
    6. New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase
    T Senoura, S Ito, H Taguchi, M Higa, S Hamada - Biochemical and , 2011 - Elsevier
     
    7. Furanosidase superfamily: Search of homologues
    DG Naumoff - Molecular Biology, 2012 - Springer
     
    8. Re-Annotation of Two Hyperthermophilic Archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638
    J Gao, J Wang - Current microbiology, 2012 - Springer
     
    9. Papaya glutamine cyclotransferase shows a singular five-fold b-propeller architecture that suggests a novel reaction mechanism
    S Garca-Pique, GE Petersen, C Lauritzen, J Pedersen - Biol. Chem, 2006 - ibmb.csic.es
     
    10. A network-based representation of protein fold space
    S Bliven - 2011 - acsweb.ucsd.edu
     
    11. Mathematical Modeling and Screening of Ligand Binding Sites in Protein using the Tetrahedral Motif Method and Double-Centroid Representation
    VM Reyes - 2012 - ritdml.rit.edu
     

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    Protein Summary


    The gene TM1225 from Thermotoga maritima encodes the NP_229030 protein from the DUF377 group (PF04041). The protein belongs to the glycosyl hydrolases 43 superfamily COG2152. The genomic neighborhood of TM1225 shows the presence (score 0.8) of a transcriptional regulator XylR-related (TM1224).

    SCOP classifies 1vkd in the all beta class, 5-bladed beta propeller fold, arabinase/levansucrase/invertase superfamily, TM1225-like family. 1vkd shows structural similarity (Dali Z=22) to many beta-xylosidases like 3cpn, 1yrz, 2exh, or 3c2u.

    Glycosyl hydrolases are a big and widespread family of enzymes that hydrolyse the glycosidic bonds between carbohydrates or between a carbohydrate and an aglycone moiety. On the basis of sequence and structural similarity, the glycoside hydrolase family belongs to the beta-fructosidase (furanosidase) family of glycosyl hydrolases [Ref].  The enzyme, most probably, acts on a furanoside residue (fructose, arabinose and ribose).

    Ligand Summary



    References

    Reviews

    References

     

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