DynDom - Protein Domain Motions

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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Status: Initialising

This morph was created using the MorphIt_Pro protein morphing technique.
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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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