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The Open Protein Structure Annotation Network
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4mru

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

    Title Crystal structure of a susD homolog (BT1281) from Bacteroides thetaiotaomicron VPI-5482 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 4mru Target Id 417751
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS82004,NP_810194.1 Molecular Weight 57521.20 Da.
    Residues 507 Isoelectric Point 4.87
    Sequence dtdmnrnkyevdseeigrenydlgstirglqglvipaqehlyqfmeamcggsyagyfgetrtgwlekys tynpktdwlkapftdvisetypkyyavlqhedapvalalakllrvtimqrvtdiygpipyskvlvsgeg sesdglnaaydsqkdvymrmfqeleeadqalednmtegnsgfeklddvyygklqqwrlflhslqlrmam rlcytdmaaeaqsiaekavtagvieknddnalfhvaenrsalcfndwkdyrvgadiicymngyadprrd kyftkvknndqegyygmriginspfsdddmitsysnrlmtasdpyvwmtasevaflraegalrkwnmgg eakdfyetgvklsfeehgasgaedylnsiaspsgytdplgsystgspanitvkwnemgeqafeenleri itqkwialfpngieswsehrrtgypkllpvvvnkgrnvsteagmrrlmypneeytqnsfhlnnainvli kessnnqggdtggthvwwdrkank
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.1757
    Matthews' coefficent 2.37 Rfactor 0.1348
    Waters 861 Solvent Content 48.04

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Update 1/15/2014: When I do a search on the HMMER website I find a full-length match to SusD-like lipoprotein families, so will probably not build a new family from this one. There appear to be many structures for this and similar families.

     

    Target id 417751 is a member of the SusD-like (PF12741) Pfam family. Shown below is a ribbons representation of the structure of target if 417751

     

    SP7807Z.png

    The structure is quite similar to several previously-determined structures of SusD. Shown in the table below are some top scoring DALI hits. Many of these are JCSG structures.

     

    PDB ID Z-score rmsd (Ang) length of alignment number of residues in related structure sequence id (%) Description
    4f53 54,4 1.4 464 498 46 Crystal structure of a susd homolog (BACOVA_04803) from Bacteroides ovatus ATCC 8483 at 2.25 A resolution (JCSG)
    3cgh 52.4 1.4 459 507 42 Crystal structure of a susd homolog (bt_3984) from bacteroides thetaiotaomicron vpi-5482 at 1.70 A resolution[Ref] (JCSG structure)
    3gzs 52.0 1.6 458 495 38 Crystal structure of a susd superfamily protein (bf3413) from bacteroides fragilis nctc 9343 at 2.10 A resolution
    3sgh 50.9 1.8 462 484 35 Crystal structure of a hypothetical susd-like protein (BT_3752) from Bacteroides thetaiotaomicron vpi-5482 at 1.70 A resolution (JCSG structure)
    4f7a 49.0 2.0 461 498 31 Crystal structure of a susd homolog (BVU_2203) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution (JCSG)
    3ehm 46.8 1.8 456 510 30 Structure of BT1043 [Ref]
    3ehn 46.5 1.9 458 512 30 BT1043 with N-acetyllactosamine[Ref]
    3p1u 40.0 2.4 437 515 24 Crystal structure of a SusD homolog (BDI_0600) from Parabacteroides distasonis ATCC 8503 AT 2.05 A resolution (JCSG structure)
    4ler 35.9 2.6 404 457 26 Crystal structure of a putative outer membrane protein, probably involved in nutrient binding (BVU_1254) from Bacteroides vulgatus ATCC 8482 at 1.42 A resolution (JCSG Structure)
    3ejn 35.2 2.8 407 450 25 CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BF3025) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.50 A RESOLUTION (JCSG Structure)

    Ligand Summary

    Reviews

    References

     

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