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The Open Protein Structure Annotation Network
PDB Keyword
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3gwr

    Title Crystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3gwr Target Id 396994
    Molecular Characteristics
    Source Thiobacillus denitrificans atcc 25259
    Alias Ids TPS24883,YP_315894.1, 3.10.450.50, 325189 Molecular Weight 15666.00 Da.
    Residues 143 Isoelectric Point 5.94
    Sequence msepvfptpeaaeeafyaafearslddmmavwarddhvacihplaaplngraavaagwrsmfgaagrfr lqvkavheirqadhvirivdefltigdetaprpailatnvyrreadgwrmvlhhasplqvgakagadtp pvvfh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.01 Rfree 0.211
    Matthews' coefficent 2.63 Rfactor 0.173
    Waters 106 Solvent Content 53.16

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gwr

    Protein Summary

    The protein YP_315894.1 is annotated as a hypothetical protein.

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    Note from PFAM:

    This protein is now in family SnoaL_2 PF12680.

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    The protein has NTF2 like fold and is structurally similar to several proteins in this family, including 10 structures solved at JCSG.

    MG11810B.png

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3cnx 17.4 2.1 120 138 28 UNCHARACTERIZED PROTEIN
    2 3d9r 15.7 2.3 116 130 18 KETOSTEROID ISOMERASE-LIKE PROTEIN
    3 2rgq 15.5 2.0 118 134 10 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE
    4 3f7s 15.4 1.9 119 142 18 UNCHARACTERIZED NTF2-LIKE PROTEIN
    5 3cu3 15.4 2.1 120 162 16 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE
    6 3bb9 14.8 2.8 115 120 14 PUTATIVE ORPHAN PROTEIN
    7 2rcd 14.8 2.1 113 128 13 UNCHARACTERIZED PROTEIN
    8 1jb5 14.7 1.9 113 123 13 NUCLEAR TRANSPORT FACTOR 2
    9 1ask 14.7 2.1 113 120 13 NUCLEAR TRANSPORT FACTOR 2
    10 1oun 14.6 2.1 113 121 13 NUCLEAR TRANSPORT FACTOR 2
    SSM Structural Homologs
    N PDB Q-score RMSD TITLE
    1 3cnx 0.5867 1.424 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (NP_825848.1) FROM STREPTOMYCES AVERMITILIS AT 2.10 A RESOLUTION
    2 3d9r 0.5817 1.624 KETOSTEROID ISOMERASE-LIKE PROTEIN (YP_049581.1) FROM ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 AT 2.40 A RESOLUTION
    3 2rgq 0.58 1.917 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE FOLD (ZP_00111510.1) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
    4 3f7s 0.5559 1.722 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (NP_746665.1) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.11 A RESOLUTION
    5 1jb4 0.5537 1.921 NTF2 M102E MUTANT
    6 2r4i 0.5502 1.902 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (YP_678039.1) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.60 A RESOLUTION
    7 3fsd 0.5494 1.941 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION IN NUTRIENT UPTAKE (YP_427473.1) FROM RHODOSPIRILLUM RUBRUM ATCC 11170 AT 1.70 A RESOLUTION
    8 3b7c 0.549 2.061 NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (NP_715767.1) FROM SHEWANELLA ONEIDENSIS AT 1.70 A RESOLUTION
    9 2rcd 0.539 1.878 UNCHARACTERIZED PROTEIN CONSERVED IN BACTERIA WITH A CYSTATIN-LIKE FOLD (YP_051588.1) FROM ERWINIA CAROTOVORA SUBSP. ATROSEPTICA SCRI1043 AT 2.32 A RESOLUTION
    10 1qma 0.5309 1.912 NUCLEAR TRANSPORT FACTOR 2 (NTF2) W7A MUTANT

     

     

    These structures are shown superimposed on this target below.

    all.pngMG11810B (green), 1ask (cyan), 1jb4 (lightmagenta), 1jb5 (yellow), 1oun (salmon), 1qma (lightgrey), 2r4i (slate), 2rcd (orange), 2rgq (lime), 3b7c (deepteal), 3bb9 (hotpink), 3cnx (yelloworange), 3cu3 (violetpurple), 3d9r(grey70), 3f7s (marine), 3fsd (olive).

     

    The protein assembles as a dimer as shown below.

    MG11810B_dimer.png

    Each of the monomer binds an unknown ligand (UNL) that srongly resembles either Benzioc acid or Nitrobenzene.

    The chemical environment around the UNL suggests that the ligand has a polar side intercating with His 42, His 122, Glu 90 and a hydrophobic side interacting with Phe 20, Leu 92, and Met 61. An unbiased solvent flattened density has been shown around UNL to justify the modeling of this ligand.

      MG11810B_UNL2.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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