Dna-Directed RNA Polymerase

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

  Property   Value
  Name Dna-Directed RNA Polymerase
  Conformer 1
(PDB)
2be5 (M)
  Conformer 2
(PDB)
1iw7 (M)
  Window Length 9
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 927 0.86   5 - 143   165 - 166   265 - 269   335 - 1115
2 184 0.61   144 - 164   167 - 264   270 - 334

Sequence


           ________________________________________________________________________________________________________________________ 
 2be5(M) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL 
         :                                                                                                                          
 1iw7(M) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL 
           ________________________________________________________________________________________________________________________ 

           ____________________143__________________164____________________________________________________________________________ 
 2be5(M) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT 
         :                                                                                                                          
 1iw7(M) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT 
           ____________________143__________________164____________________________________________________________________________ 

           ___________________262_____________________________________________________________________334__________________________ 
 2be5(M) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML 
         :                                                                                                                          
 1iw7(M) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML 
           ___________________262_____________________________________________________________________334__________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT 
         :                                                                                                                          
 1iw7(M) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
         :                                                                                                                          
 1iw7(M) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
         :                                                                                                                          
 1iw7(M) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 
         :                                                                                                                          
 1iw7(M) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 
         :                                                                                                                          
 1iw7(M) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2be5(M) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS 
         :                                                                                                                          
 1iw7(M) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS 
           ________________________________________________________________________________________________________________________ 

           _______________________________________                                                                                  
 2be5(M) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR                                                                                  
         :                                                                                                                          
 1iw7(M) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR                                                                                  
           _______________________________________                                                                                  

Morph

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Status: Initialising

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
5.1
Translation
(A)
0.1
Closure
(%)
85.4
Bending Residues
( green )
  143 - 144
  164 - 167
  262 - 276
  334 - 335
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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