DynDom - Protein Domain Motions

RNA Polymerase Beta Subunit

(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	RNA Polymerase Beta Subunit
Conformer 1 (PDB)	1iw7 (D)
Conformer 2 (PDB)	1l9z (D)
Window Length	13
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	1116	3.76	9 - 48 80 - 132 157 - 1493
2	31	6.7	49 - 79

Sequence

`___________________________________________46_______________________________79__________________________________________` `1iw7(D) : KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT` `:` `1l9z(D) : KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT` `___________________________________________46_______________________________79__________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : ELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEI` `:` `1l9z(D) : ELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEE------------------------------------------------------------------------------------` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) :` `LAELPEPYLFgDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEAL` `:` `1l9z(D) :` `---------------------------------------------------------------------------------------------------dARMGAEAIQELLKELDLEKL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : EKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTN` `:` `1l9z(D) : ERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : PGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI` `:` `1l9z(D) : PGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRE` `:` `1l9z(D) : QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : TSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDD` `:` `1l9z(D) : TSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : AVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS` `:` `1l9z(D) : AVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : SHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLT` `:` `1l9z(D) : SHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : CQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLV` `:` `1l9z(D) : CQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRT----------------pRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(D) : KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKS` `:` `1l9z(D) : KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIA---vPVAWKPLLMGVTKSALSTKS` `________________________________________________________________________________________________________________________` `________________________________________________________________________` `1iw7(D) : WLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA` `:` `1l9z(D) : WLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIEEAR*****` `________________________________________________________________________`

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)	170.8
Translation (A)	-1.2
Closure (%)	79.3
Bending Residues ( green )	46 - 49 79 - 87
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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