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)
1i6v (C)
  Conformer 2
(PDB)
2be5 (M)
  Window Length 7
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1050 3.23   5 - 472   530 - 1112
2 21 4.52   473 - 486   523 - 529

Sequence


           ________________________________________________________________________________________________________________________ 
 1i6v(C) : *KIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPL 
         :                                                                                                                          
 2be5(M) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFT 
         :                                                                                                                          
 2be5(M) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : LLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMV 
         :                                                                                                                          
 2be5(M) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML 
           ________________________________________________________________________________________________________________________ 

           __________________________________________________________________________________________________________469___________ 
 1i6v(C) : MGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVT 
         :                                                                                                                          
 2be5(M) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT 
           __________________________________________________________________________________________________________469___________ 

           ______________________________________________529_______________________________________________________________________ 
 1i6v(C) : EEVVYMTASEEDRYTIAQANTPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
         :                                                                                                                          
 2be5(M) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
           ______________________________________________529_______________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : GEVVKVDGTRIAVRYEDGRLV-HPLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
         :                                                                                                                          
 2be5(M) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : RITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLA 
         :                                                                                                                          
 2be5(M) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSPE 
         :                                                                                                                          
 2be5(M) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6v(C) : EQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPS 
         :                                                                                                                          
 2be5(M) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS 
           ________________________________________________________________________________________________________________________ 

           _______________________________________                                                                                  
 1i6v(C) : VPESFRVLVKELQALALDVQTLDEKDNPVDVFEGL****                                                                                  
         :                                                                                                                          
 2be5(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)
60.5
Translation
(A)
-2.5
Closure
(%)
94.0
Bending Residues
( green )
  469 - 473
  529 - 530
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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