Riboflavin biosynthesis protein ribD
Ligand-induced domain movement details

Jmol view of liganded conformation 1

Domain Movement

domain 1 is binding domain(fixed in space) domain 2 is binding domain(fixed in space)

Sequence


           __________________________________________________ 
 2d5n(B) : MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHA 
         :                                                    
 2d5n(A) : MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHA 
           __________________________________________________ 

           __________________________________________________ 
 2d5n(B) : EVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMR 
         :                                                    
 2d5n(A) : EVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMR 
           __________________________________________________ 

           _________________________________136______________ 
 2d5n(B) : DPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTL 
         :                                                    
 2d5n(A) : DPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTL 
           _________________________________136______________ 

           __________________________________________________ 
 2d5n(B) : KAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADN 
         :                                                    
 2d5n(A) : KAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADN 
           __________________________________________________ 

           __________________________________________________ 
 2d5n(B) : PSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEE 
         :                                                    
 2d5n(A) : PSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEE 
           __________________________________________________ 

           __________________________________________________ 
 2d5n(B) : KKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFV 
         :                                                    
 2d5n(A) : KKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFV 
           __________________________________________________ 

           __________________________________________________ 
 2d5n(B) : KEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGR 
         :                                                    
 2d5n(A) : KEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGR 
           __________________________________________________ 

           _________                                          
 2d5n(B) : DIKLTAKPT                                          
         :                                                    
 2d5n(A) : DIKLTAKPT                                          
           _________                                          

Details

  Property   Value
 Conformer 1 2d5n(B)
 Conformer 2 2d5n(A)
 Radius gyration for conformer 1 23.55 A
 Radius gyration for conformer 2 23.35 A
 EC Number 3.5.4.26   1.1.1.193  
Click here to see the DynDom results or the famliy
 Trigger ligands NDP381
 Trigger ligands in which conformation Conformation  1
 Conformaton with trigger ligands is compact No
 Spanning ligands No
 Residues in enzyme contacting ligands ALA152  ALA153  ALA294  ASP199  GLU290  GLY165  GLY192  GLY194  GLY291  GLY292  ILE160  ILE270  ILE272  LEU219  SER293  SER298  THR195  THR221  VAL193  VAL222  VAL295 
 Residues in extended bending regions contacting ligands Null
 Residues in extended bending regions making H-bonds or salt-bridges with ligands Null
  Residues in extended bending regions with an H-bond between its main chain and ligands Null
Click here to see the details of H-bonds between ligands and enzyme in PDF format generated by LIGPLOT