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The Open Protein Structure Annotation Network
PDB Keyword
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3hc1

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

    Title Crystal structure of HDOD domain protein with unknown function (NP_953345.1) from GEOBACTER SULFURREDUCENS at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3hc1 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS25312,NP_953345.1, _0037.000821_, 326954
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.35 Rfactor 0.180
    Waters
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    Solvent Content 47.75

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3hc1
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)
    S Mulepati, S Bailey - Journal of Biological Chemistry, 2011 - ASBMB
     
    3. Tetrahydrofuro (3, 2-B) pyrrol-3-one derivatives as inhibitors of cysteine proteinases
    M Quibell, JP Watts - US Patent 7,799,791, 2010 - Google Patents
     

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    Protein Summary

    Gene Sama_3455 from Geobacter sulfurreducens encodes the NP_953345 protein, a member of so-called HD family of metal phospho-hydrolases (PF08668).

    SCOP classifies 3hc1 in the all alpha class, HD-domain/PDEase-like superfamily, modified HD domain family. DALI top hits are with the putative metal dependent phosphohydrolase 3i7a (Z=17), the CJ0248 protein 1vqr (Z=12) and the MMOQ response regulator 3ljx (Z=12). The overall structure of 3hc1 is similar to 1vqr (rmsd 3.01A for 181 Ca, seq identity 10%, sequence only alignment 25% identical residues 19-215 per BLAST). Unlike 1vqr which has lost the metal binding site, 3hc1 is expected to be a functional enzyme with an intact metal site for dual binding.

     

    Figure 1: Monomer of 3hc1 (metals shown as spheres)

    mh5158b-monomer.png

    Figure 2: The putative active site pocket on the surface of the protein

    mh5158b-active.png

     

    References:

    Aravind L, Koonin EV; , Trends Biochem Sci 1998;23:469-472.: The HD domain defines a new superfamily of metal-dependent phosphohydrolases. PUBMED:9868367

    Ligand Summary

     

    2 Fe ions

    Reviews

    References

     

    No references found.

    Tag page

    Files (2)

    FileSizeDateAttached by 
     mh5158b-active.png
    mh5158b active site
    202.13 kB22:54, 30 Mar 2009qxuActions
     mh5158b-monomer.png
    mh5158b monomer
    101.59 kB22:54, 30 Mar 2009qxuActions
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