.
The Open Protein Structure Annotation Network
PDB Keyword
.

3klb

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

    Title Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3klb Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS7529,YP_213683.1, 60683539, 87515
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 1
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 3.06 Rfactor 0.148
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 59.84

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3klb

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Target ID 388560 encodes a 18.1 kDa protein encoded by Bacteroides fragilis NCTC 9343. The protein contains one FMN in the molecule, and belongs to the new Pfam family of Flavodoxin_4 (PF12682) in the Flavoprotein clan (CL0042).

    monomer.png

     

    Figure 1. Target ID 388560 contains one monomer (biomolecule) in asu. 

                   Ribbon is shown as color-coded as N-terminal region in blue and the C-terminal region in red.

                   FMN is shown as red stick.

     

    Dali hits are:

     

       No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3edo-B 17.5 2.2 142 149 24 PDB MOLECULE: PUTATIVE TRP REPRESSOR BINDING PROTEIN; 2: 3edo-A 17.4 2.3 143 151 23 PDB MOLECULE: PUTATIVE TRP REPRESSOR BINDING PROTEIN; 3: 1nni-1 12.3 2.5 127 171 20 PDB MOLECULE: HYPOTHETICAL PROTEIN YHDA; 4: 3gfs-C 12.2 2.5 127 169 20 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 5: 3gfs-D 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 6: 3gfs-I 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 7: 3gfr-A 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 8: 3gfq-B 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 9: 3gfq-A 12.0 2.6 126 168 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 10: 3gfs-K 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 11: 3gfs-J 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 12: 3gfs-G 12.0 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 13: 3gfs-L 12.0 2.5 125 166 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 14: 3gfs-H 12.0 2.5 125 166 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 15: 4nll 12.0 2.8 122 138 17 PDB MOLECULE: FLAVODOXIN; 16: 5nll-A 12.0 2.8 121 138 16 PDB MOLECULE: FLAVODOXIN; 17: 2fvx 12.0 2.8 122 137 17 PDB MOLECULE: FLAVODOXIN; 18: 3gfr-D 11.9 2.5 125 172 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 19: 3gfr-C 11.9 2.5 125 167 21 PDB MOLECULE: FMN-DEPENDENT NADPH-AZOREDUCTASE; 20: 2gsw-C 11.9 2.5 124 168 21 PDB MOLECULE: YHDA;

    The top Dali hit (3edo) is  also a JCSG target. The superposition between 388560 and 3edo are shown as below.

     

    super_3edo.png

    Figure 2. Superposition of 388560 (green) with 3edo (light blue). The structures near FMN binding sites are

                   somewhat different betwen two structures (top of the figure).

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (2)

    FileSizeDateAttached by 
     monomer.png
    No description
    175.61 kB05:20, 17 Oct 2009gyewonActions
     super_3edo.png
    No description
    214.97 kB05:20, 17 Oct 2009gyewonActions
    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