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                                                                             
           ____________________________________________                                                                             

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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

PyMOL Script

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