.
The Open Protein Structure Annotation Network
PDB Keyword
.

3qi7

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

    Title Crystal structure of a Putative transcriptional regulator (YP_001089212.1) from Clostridium difficile 630 at 1.86 A resolution. To be published
    Site JCSG
    PDB Id 3qi7 Target Id 390377
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS7720,YP_001089212.1, 85852 Molecular Weight 41786.65 Da.
    Residues 370 Isoelectric Point 4.91
    Sequence gkkdkekiiddfkvavvtqplsenkvqynmveemakeyeeenkidkdkdgqtkvkqtikhvvlpenfts nidsainkivkladdkevqaivvstdqagllpalqkvkekrpeiitisapmgddknqlsqfvdvnlgvs aeergkvlaerskemgakafihyastddlkdvniakrlemiketckniglpfvqvntpninteedknkv kqflnediekqvkkygkdinvfgvneymdeviltkalelkyivaeqsnpspiqtypsvmglkisekdaq nydkindmisekakafgmsnrlggypmpmdaflpslaiylatemvkqdltqedvcdpdyleaftelrfg igseftpltevlynyqsvilsqliy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.86 Rfree 0.2202
    Matthews' coefficent 2.37 Rfactor 0.1897
    Waters 560 Solvent Content 48.01

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3qi7

    Protein Summary

    This protein is likely a nutrient binding protein, open conformation. It consists of two domains (162:329 and the rest). The two domains are somewhat similar in fold (3.1A for 94 aligned Ca atoms). The overall structure resembles that sugar binding domain of ABC transporters (3c6q etc), as a result, we may hypothesize that this protein may bind some kind of sugar.

     

    Notes from PFAM:

    DUF3798 (PF12683). It is likely to be related to Periplasmic binding domain families such as Bmp (PF02608) which gives a strong suggestion as to its broad function.

     

    Fig 1. monomer

    gs13199a.png

     

    Fig 2. Dali results

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  3c6q-B 18.5  3.7  271   305   11 PDB  MOLECULE: SUGAR ABC TRANSPORTER, PERIPLASMIC SUGAR-BINDING           
       2:  3c6q-A 18.5  3.7  271   305   11 PDB  MOLECULE: SUGAR ABC TRANSPORTER, PERIPLASMIC SUGAR-BINDING           
       3:  1tm2-A 17.8  4.5  274   314    9 PDB  MOLECULE: SUGAR TRANSPORT PROTEIN;                                   
       4:  1gub-A 17.7  4.3  264   288   12 PDB  MOLECULE: D-ALLOSE-BINDING PERIPLASMIC PROTEIN;                      
       5:  1gud-B 17.7  4.0  260   288   13 PDB  MOLECULE: D-ALLOSE-BINDING PERIPLASMIC PROTEIN;                      
       6:  1gud-A 17.6  4.1  260   288   13 PDB  MOLECULE: D-ALLOSE-BINDING PERIPLASMIC PROTEIN;                      
       7:  3g1w-B 17.4  4.3  257   290   10 PDB  MOLECULE: SUGAR ABC TRANSPORTER;                                     
       8:  3h6g-A 16.7  4.2  285   377   12 PDB  MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2;                  
       9:  2fn9-B 16.7  4.1  247   280   11 PDB  MOLECULE: RIBOSE ABC TRANSPORTER, PERIPLASMIC RIBOSE-                
      10:  3h6g-B 16.6  4.2  284   383   12 PDB  MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2;                  
      11:  2wrz-A 16.6  5.0  255   299   13 PDB  MOLECULE: L-ARABINOSE-BINDING PERIPLASMIC PROTEIN;                   
      12:  1ba2-B 16.6  4.5  248   271   12 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      13:  3hut-A 16.5  4.0  280   346   10 PDB  MOLECULE: PUTATIVE BRANCHED-CHAIN AMINO ACID ABC                     
      14:  1urp-C 16.5  4.6  246   271   10 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      15:  1urp-B 16.5  4.5  245   271   11 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      16:  1urp-A 16.5  4.4  245   271   10 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      17:  1urp-D 16.5  4.6  246   271   10 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      18:  3h6h-A 16.4  4.4  285   383   12 PDB  MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2;                  
      19:  3h6h-B 16.4  4.4  286   379   12 PDB  MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2;                  
      20:  1ba2-A 16.4  4.7  246   271   12 PDB  MOLECULE: D-RIBOSE-BINDING PROTEIN;                                  
      21:  2fn9-A 16.4  3.8  250   280   11 PDB  MOLECULE: RIBOSE ABC TRANSPORTER, PERIPLASMIC RIBOSE-                
      22:  2liv-A 16.3  4.7  282   344   11 PDB  MOLECULE: LEUCINE;                                                   
      23:  3g1w-A 16.2  4.6  252   291   10 PDB  MOLECULE: SUGAR ABC TRANSPORTER;                                     
      24:  2liv   16.2  4.7  277   344   11 PDB LEUCINE(SLASH)*ISOLEUCINE(SLASH)*VALINE-BINDING PROTEIN               
      25:  2fw0-A 16.2  3.4  263   305   11 PDB  MOLECULE: D-GALACTOSE-BINDING PERIPLASMIC PROTEIN;                   
      26:  1gcg   16.2  4.6  262   309   11 PDB GALACTOSE/GLUCOSE-BINDING PROTEIN (CLOSED, UNLIGANDED FORM)           
      27:  1gcg-A 16.2  4.6  262   309   11 PDB  MOLECULE: GALACTOSE/GLUCOSE-BINDING PROTEIN;                         
      28:  1z18-A 16.2  5.0  274   344   11 PDB  MOLECULE: LEU/ILE/VAL-BINDING PROTEIN;                               
      29:  3h5l-A 16.1  3.8  279   397    6 PDB  MOLECULE: PUTATIVE BRANCHED-CHAIN AMINO ACID ABC                     
      30:  2fvy-A 16.0  4.6  261   305   12 PDB  MOLECULE: D-GALACTOSE-BINDING PERIPLASMIC PROTEIN;                   
      31:  1z17-A 16.0  5.1  274   344   11 PDB  MOLECULE: LEU/ILE/VAL-BINDING PROTEIN;                               
      32:  1z16-A 16.0  5.1  273   344   12 PDB  MOLECULE: LEU/ILE/VAL-BINDING PROTEIN;                               
      33:  2qw1-A 16.0  3.7  265   305   12 PDB  MOLECULE: D-GALACTOSE-BINDING PERIPLASMIC PROTEIN;                   
      34:  1gca-A 15.9  4.7  261   309   11 PDB  MOLECULE: GLUCOSE/GALACTOSE-BINDING PROTEIN;                         
      35:  3gbp   15.8  4.6  259   305   10 PDB GALACTOSE-BINDING PROTEIN COMPLEX WITH GLUCOSE                        
      36:  3gbp-A 15.8  4.6  259   305   10 PDB  MOLECULE: GALACTOSE-BINDING PROTEIN;                                 
      37:  2ipl-A 15.8  4.8  260   306   12 PDB  MOLECULE: D-GALACTOSE-BINDING PERIPLASMIC PROTEIN;                   
      38:  2lbp   15.8  4.6  282   346   11 PDB LEUCINE-BINDING PROTEIN (/LBP$)                                       
      39:  2lbp-A 15.8  4.4  284   346   11 PDB  MOLECULE: LEUCINE-BINDING PROTEIN; 

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (1)

    FileSizeDateAttached by 
     gs13199a.png
    gs13199a
    156.92 kB20:22, 23 Nov 2009qxuActions
    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