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)	1ynj (D)
Conformer 2 (PDB)	1hqm (D)
Window Length	11
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	871	6.21	8 - 133 442 - 1235
2	21	10.66	161 - 441

Sequence

`_________________________________________________________________________________________________________110____________` `1ynj(D) : KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATE` `:` `1hqm(D) : KEVRKVRIALASPEKIRSWSYGEVEKPET-------------------------------------eGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATE` `_________________________________________________________________________________________________________110____________` `________________________________________________________________________________________________________________________` `1ynj(D) : LEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDGVALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVL` `:` `1hqm(D) : LEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDxXXXXXXXXxXXXX-------------------------------------------------------------------------` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) :` `AELSEPYLFRAEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVGQPLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHMNVIVPEGAKVQ` `:` `1hqm(D) :` `------------------------------------------------------------------------------------------------------------------------` `________________________________________________________________________________________________________________________` `____________________________________________________________________________441_________________________________________` `1ynj(D) :` `AGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLERELLEEMK` `:` `1hqm(D) :` `-------------------------------------------------------------------XXXXXXXXXXXXXXXXXXXXXXiDARMGAEAIQELLKELDLEKLERELLEEMK` `____________________________________________________________________________36U_________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : HPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRS` `:` `1hqm(D) : HPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPD------------aTSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVE` `:` `1hqm(D) : LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : GQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFV` `:` `1hqm(D) : GQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : FANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGI-TIGIDDAVIPEEKQ` `:` `1hqm(D) : FANPDEALLAVAHGLLDLQDTVTTRYLGRRLETNPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : RYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG` `:` `1hqm(D) : RYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : ADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVC` `:` `1hqm(D) : ADTALRTADSGYLTRKLVDVAHEIVVREADCGTTKYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVC` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : QKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRT*******************************************************************************` `:` `1hqm(D) : QKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTgTDITQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ynj(D) : ********************************************************************************************************************` `:` `1hqm(D) : IDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAvPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAI` `________________________________________________________________________________________________________________________` `____________________________________________` `1ynj(D) : ******************************************` `:` `1hqm(D) : AGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIE` `____________________________________________`

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)	103.8
Translation (A)	34.6
Closure (%)	38.9
Bending Residues ( green )	110 - 161 441 - 451
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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