The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution. To be Published
    Site JCSG
    PDB Id 3m1u Target Id 405735
    Molecular Characteristics
    Source Desulfovibrio vulgaris subsp. vulgaris str. hildenborough
    Alias Ids TPS31041,YP_010117.1, PF00877 Molecular Weight 46938.95 Da.
    Residues 433 Isoelectric Point 8.63
    Sequence srpatppvtppsreghvadldrfpqdlrvyamkagadrqllpfteqaaqdarwnrrffapwrmtrisvp vkdvaapfgtdgrprgyaenllpwdvtrwgalasgaaldlypsqawkgivvsnsalrevptlrpmftap tragqgypfdmfqrtavwmgtpvfvghatadrawlyvetafaagwmpaadvarvddafmtryesgslaa ilrddtslngadgthlatahigtvlplsgasqvgrtvlvpvrapeghavvvpvlltsgeaaqkpvpltp gnmaelgnrmmgqpygwgglyedrdcsstlrdlftpfglwlprnsasqakagryvdiakldaddkeari vaegvpfmtllwlrghitlylglhegqaamfhnmwgirthrggvegryvlgravvtstrpgldvpgndn adgllgrmqgmsilpggaq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.75 Rfree 0.173
    Matthews' coefficent 2.08 Rfactor 0.139
    Waters 946 Solvent Content 40.74

    Ligand Information


    Google Scholar output for 3m1u

    Protein Summary

    Gene DVU_0896 from Desulfovibrio vulgaris hildenborough encodes the YP_010117 protein that belongs to the NlpC/P60 domain family (PF00877).

    3m1u structure corresponds to the 32-464 fragment of YP_010117 and contains four domains: the N1 domain (1:145), SH3b1, SH3b2 and a catalytic domain at the C-terminus.  The SH3-like domain reveals SH3-like barrel fold type SCOP50036, while the NlpC/P60 domain belongs to the cysteine proteinases fold type SCOP54000. DALI top hits are with 3h41, 2evr, 2hbw, and 2fg0.

    3m1u is another member of the N-terminal SH3b domain + C-terminal NlpC/P60 domain group solved by JCSG (together with 2evr and 3h41). The structure series 2evr -->3h41--->3m1u show an increasing order of complexity, but with similar putative active sites. The N1 domain, that wraps around the SH3b1 and the catalytic domain, seems to function as a stablizing factor of the two interacting domain.


    Figure. 1. 3m1u structure with each domain depicted in a different color



    Ligand Summary




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