Dna-Directed RNA Polymerase Beta Chain

(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 Beta Chain
  Conformer 1
(PDB)
1iw7 (M)
  Conformer 2
(PDB)
1iw7 (C)
  Window Length 7
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 211 0.16   572 - 577   670 - 702   834 - 1002   1006 - 1008
2 104 0.22   471 - 571   666 - 668
3 548 0.6   4 - 456   578 - 665   804 - 807   813 - 815
4 126 0.37   703 - 803   808 - 812   816 - 832   1003 - 1005
5 108 0.2   1009 - 1116

Sequence


           ________________________________________________________________________________________________________________________ 
 1iw7(M) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL 
         :                                                                                                                          
 1iw7(C) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1iw7(M) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT 
         :                                                                                                                          
 1iw7(C) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1iw7(M) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML 
         :                                                                                                                          
 1iw7(C) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML 
           ________________________________________________________________________________________________________________________ 

           _____________________________________________________________________________________________456________________________ 
 1iw7(M) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT 
         :                                                                                                                          
 1iw7(C) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT 
           _____________________________________________________________________________________________456________________________ 

           ________________________________________________________________________________________571_____________________________ 
 1iw7(M) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
         :                                                                                                                          
 1iw7(C) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED 
           ________________________________________________________________________________________571_____________________________ 

           _______________________________________________________________666_________________________________702__________________ 
 1iw7(M) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
         :                                                                                                                          
 1iw7(C) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE 
           _______________________________________________________________666_________________________________702__________________ 

           ________________________________________________________________________________803_807__812_________________832________ 
 1iw7(M) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 
         :                                                                                                                          
 1iw7(C) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 
           ________________________________________________________________________________803_807__812_________________832________ 

           ________________________________________________________________________________________________________________________ 
 1iw7(M) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 
         :                                                                                                                          
 1iw7(C) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 
           ________________________________________________________________________________________________________________________ 

           _____________________________________1001_1006__________________________________________________________________________ 
 1iw7(M) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS 
         :                                                                                                                          
 1iw7(C) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS 
           _____________________________________1001_1006__________________________________________________________________________ 

           _______________________________________                                                                                  
 1iw7(M) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR                                                                                  
         :                                                                                                                          
 1iw7(C) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR                                                                                  
           _______________________________________                                                                                  

Morph

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 4.0 -0.4 97.9   571 - 577   666 - 671 Bending Region Analysis
1 3 2.8 -0.5 87.6   572 - 578 Bending Region Analysis
1 4 4.8 -0.4 98.0   702 - 707   832 - 834   1001 - 1008 Bending Region Analysis
1 5 2.5 0.1 4.8   1006 - 1009 Bending Region Analysis
3 2 2.2 0.0 75.4   456 - 472   665 - 668 Bending Region Analysis
3 4 3.7 0.2 90.7   803 - 805   807 - 808   812 - 813   815 - 816 Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 1 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 3 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 3

Movement classification: Hinge

Conformer 1 Contact:
Residue 3 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 3

Movement classification: Hinge

PyMOL Script

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