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)
2a69 (N)
  Conformer 2
(PDB)
2be5 (D)
  Window Length 9
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1069 0.68   6 - 773   775 - 775   1090 - 1501
2 173 0.11   774 - 774   776 - 947
3 27 0.41   1063 - 1089
4 115 0.44   948 - 1062

Sequence


           ________________________________________________________________________________________________________________________ 
 2a69(N) : KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT 
         :                                                                                                                          
 2be5(D) : KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : ELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEI 
         :                                                                                                                          
 2be5(D) : ELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEI 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : LAELPEPYLFgDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEAL 
         :                                                                                                                          
 2be5(D) : LAELPEPYLFgDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEAL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : EKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTN 
         :                                                                                                                          
 2be5(D) : EKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTN 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : PGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI 
         :                                                                                                                          
 2be5(D) : PGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI 
           ________________________________________________________________________________________________________________________ 

           _________________________________________________________773____________________________________________________________ 
 2a69(N) : QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRE 
         :                                                                                                                          
 2be5(D) : QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRE 
           _________________________________________________________773____________________________________________________________ 

           _____________________________________________________________________________________________________________945________ 
 2a69(N) : TSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDD 
         :                                                                                                                          
 2be5(D) : TSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDD 
           _____________________________________________________________________________________________________________945________ 

           _________________________________________________________________________________________________________1062___________ 
 2a69(N) : AVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS 
         :                                                                                                                          
 2be5(D) : AVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFIS 
           _________________________________________________________________________________________________________1062___________ 

           ___________1088_________________________________________________________________________________________________________ 
 2a69(N) : SHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLT 
         :                                                                                                                          
 2be5(D) : SHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLT 
           ___________1088_________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : CQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLV 
         :                                                                                                                          
 2be5(D) : CQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2a69(N) : KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKS 
         :                                                                                                                          
 2be5(D) : KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________                                                 
 2a69(N) : WLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA                                                 
         :                                                                                                                          
 2be5(D) : WLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA                                                 
           ________________________________________________________________________                                                 

Morph

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 3.4 -0.2 8.1   773 - 778 Bending Region Analysis
1 3 3.0 1.1 30.2   1088 - 1094 Bending Region Analysis
4 2 1.2 -1.0 61.8   945 - 948 Bending Region Analysis
4 3 1.3 1.0 10.0   1062 - 1063 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 4 ———› Residue 2

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

Movement classification: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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