The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of dimeric protein of unknown function and ferredoxin-like fold (YP_212648.1) from Bacteroides fragilis NCTC 9343 at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3fmb Target Id 391626
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS20915,YP_212648.1,, 325252 Molecular Weight 11279.45 Da.
    Residues 99 Isoelectric Point 5.13
    Sequence mvkhivlfklrddvpveeklvvmnsfkeaiealpakisvirkievglnmnpgetwnialysefdnlddv kfyathpehvaagkilaetkesracvdyef
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.85 Rfree 0.205
    Matthews' coefficent 3.19 Rfactor 0.170
    Waters 296 Solvent Content 61.40

    Ligand Information


    Google Scholar output for 3fmb

    Protein Summary

    Pfam update: This protein is now in Family: Dabb (PF07876) which has several other structures,


    391626 belongs to Pfam; PF07876; Dabb;stress responsive A/B Barrel Domain. The function is unknown.

    There is a dimer found in the crystallographic asu. Crystal packing analysis suggests that this dimer should be the stable oligomeric form in solution.


     Fig 1. A dimer in the crystallographic asu.

    Several JCSG structures are similar to this protein (by DALI). They are 3bgu (1.8A rmsd, 97 Ca aligned, 25% id) , 3qyc (2.4A rmsd, 98 Ca aligned, 17% id) and 3bb5 (2.3A rmsd, 97 Ca aligned, 22% id). The superposition of 391626 with 3bgu, 2qyc and 3bb5 is shown as below.



     Fig 2. Superposition of 391626 monomer (green) with that of 3bgu (pale green), 2qyc (light blue) and 3bb5 (pale yellow).


    Based on the above related structure, it is possible that the active site is located in the region near where the SO4-3 is bound. This region is also occupied by NBZ,EDO (3bgu), EDO (2qyc) and EDO (3bb5) as shown below.


    Fig 3. Superposition of the ligands in the presumable active site of 391626 3bgu, 2qyc  and 3bb5 (color scheme is the same as above Fig 2).

    Ligand Summary

    SO4 and EDO were found in the structure.




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