.
The Open Protein Structure Annotation Network
PDB Keyword
.

4nzj

    Title Crystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution. To be published
    Site JCSG
    PDB Id 4nzj Target Id 419777
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS82719,YP_211072.1 Molecular Weight 53200.52 Da.
    Residues 476 Isoelectric Point 5.35
    Sequence gdvvlkvfegkprinsphiignypstpfifyiptsgqrpmqwsaeklpegleldsktgiisgvmtskgd ytvtlkaenalgvsvkqlvirigdellltppmgwnswntfgqhlteelvlqtadamitngmrdlgysyi niddfwqlpergadghlqidktkfprgikyvadylhergfklgiysdaaektcggvcgsygyeetdakd faswgvdllkydycnapvdrveameryakmgralratnrsivysvcewgqrepwkwakqvgghlwrvsg digdiwyrdgnrvgglhgilnileinaplseyagpsgwndpdmlvvgidgksmsigyesegctqeqyks hfslwcmmaspllsgndvrnmndstlkilldpdliainqdvlgrqaersirsdhydiwvkpladgrkav acfnrasspqtvilnentiadlsfeqiycldnhltksgsdskelivklapyqckvyifgktd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.57 Rfree 0.1685
    Matthews' coefficent 2.35 Rfactor 0.1541
    Waters 488 Solvent Content 47.62

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The protein YP_211072.1 is annotated as putative alpha-galactosidase. YP_211072.1 belongs to PFAM PF10632 He_PIG_assoc PF05345 He_PIG. This domain has been named NEW1 but its actual function is not known. It is found on proteins which are bacterial galactosidases . The domain is associated with the He_PIG family, PF05345 a putative Ig-containing domain.

     

    The monomer structure is shown below in rainbow representation. A glycerol molecule (red sticks) is bound at the putative active site.

    SP3088C.png

    Top 10 DALI Structural Homologs
     
    N PDB Z-score RMSD LALI NRES %ID Description
    1 1uas 47.7 1.6 356 362 41 Alpha-galactosidase
    2 3a5v 46.0 1.6 365 397 36 Alpha-galactosidase
    3 3s5z 43.3 1.8 361 390 36 Alpha-galactosidase a
    4 3lx9 43.3 1.8 360 390 36 Alpha-galactosidase a
    5 3s5y 43.2 1.8 360 390 36 Alpha-galactosidase a
    6 3lxc 43.1 1.8 360 390 36 Alpha-galactosidase a
    7 3tv8 42.9 1.8 361 390 35 Alpha-galactosidase a
    8 3hg5 42.9 1.8 361 391 36 Alpha-galactosidase a
    9 3hg4 42.9 1.8 360 390 36 Alpha-galactosidase a
    10 3hg2 42.9 1.7 358 390 36 Alpha-galactosidase a

     

    A superposition of YP_211072.1 (green) on 1uas (magenta) confirms the annotation of this protein as Alpha-galactosidase.

    SP3088C_1uas.png

    YP_211072.1 structure has an additional domain at the N-terminus that is absent in 1uas.

     

    The glycerol (green sticks) in YP_211072.1 is bound at the same location as Alpha D-galactose (magenta sticks) in 1uas.

    as.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch