Dna-Directed RNA Polymerase II Largest 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 Dna-Directed RNA Polymerase II Largest Subunit
  Conformer 1
(PDB)
2e2h (A)
  Conformer 2
(PDB)
1y1v (A)
  Window Length 13
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1365 2.08   8 - 1075   1086 - 1089   1101 - 1439
2 21 6.0   1076 - 1085   1090 - 1100

Sequence


           ________________________________________________________________________________________________________________________ 
 2e2h(A) : VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
         :                                                                                                                          
 1y1v(A) : VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSE-----lVSRGGCGNTQPTIRKDGLKLVGSW-----lRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPS 
         :                                                                                                                          
 1y1v(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKdEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : ISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQA----gRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKS 
         :                                                                                                                          
 1y1v(A) : ISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : IAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNL 
         :                                                                                                                          
 1y1v(A) : IAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : HVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID 
         :                                                                                                                          
 1y1v(A) : HVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKA 
         :                                                                                                                          
 1y1v(A) : GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKA 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : GRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIM 
         :                                                                                                                          
 1y1v(A) : GRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIM 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : VHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQ 
         :                                                                                                                          
 1y1v(A) : VHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQ 
           ________________________________________________________________________________________________________________________ 

           ___________________________________________________________________________________________________1072_________1085____ 
 2e2h(A) : TFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGV 
         :                                                                                                                          
 1y1v(A) : TFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGV 
           ___________________________________________________________________________________________________1072_________1085____ 

           _______1100_____________________________________________________________________________________________________________ 
 2e2h(A) : ASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLqQSPWLLRLELDRAAMNDKDLTMGQVGERIKQT 
         :                                                                                                                          
 1y1v(A) : ASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLqQSPWLLRLELDRAAMNDKDLTMGQVGERIKQT 
           _______1100_____________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2e2h(A) : FKNDLFVIWSED----lIIRCRVVaEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALY 
         :                                                                                                                          
 1y1v(A) : FKNDLFVIWSEDNDEKLIIRCRVVaEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALY 
           ________________________________________________________________________________________________________________________ 

           __________________________________________________________________________________________________________               
 2e2h(A) : KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI**********               
         :                                                                                                                          
 1y1v(A) : KEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMP               
           __________________________________________________________________________________________________________               

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
33.7
Translation
(A)
-0.9
Closure
(%)
95.0
Bending Residues
( green )
  1072 - 1076
  1085 - 1090
  1100 - 1101
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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