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)
1i6h (A)
  Conformer 2
(PDB)
1k83 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1030 1.16   332 - 1388   1400 - 1401   1434 - 1443
2 317 1.28   7 - 331   1389 - 1399   1402 - 1433

Sequence


           ________________________________________________________________________________________________________________________ 
 1i6h(A) : VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
         :                                                                                                                          
 1k83(A) : ***QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPE---------kIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPS------lVSRGGCGNTQPTIRKDGLKLVGSWK----lRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPS 
         :                                                                                                                          
 1k83(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKePELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVR-- 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________329_______________________________________________________ 
 1i6h(A) : eDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQApVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYN 
         :                                                                                                                          
 1k83(A) : -dDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQ------sIRARLKGKEGRI--------vDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYN 
           ______________________________________________________________329_______________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : IDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQL 
         :                                                                                                                          
 1k83(A) : IDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : CAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGS 
         :                                                                                                                          
 1k83(A) : CAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : SNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVK 
         :                                                                                                                          
 1k83(A) : SNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : QMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVI 
         :                                                                                                                          
 1k83(A) : QMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVI 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : QFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIK 
         :                                                                                                                          
 1k83(A) : QFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : DIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLkKVTSGVPRLKEILNVAKNMKTP 
         :                                                                                                                          
 1k83(A) : DIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLkKVTSGVPRLKEILNVAKNMKTP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : SLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLqQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVa 
         :                                                                                                                          
 1k83(A) : SLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS-qQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVa 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i6h(A) : EEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV 
         :                                                                                                                          
 1k83(A) : EEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV 
           ________________________________________________________________________________________________________________________ 

           _____1383__________1397________________________________1433_________________                                             
 1i6h(A) : MTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI*****                                             
         :                                                                                                                          
 1k83(A) : MTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESL                                             
           _____1383__________1397________________________________1433_________________                                             

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)
29.5
Translation
(A)
0.9
Closure
(%)
81.4
Bending Residues
( green )
  329 - 347
  1383 - 1394
  1397 - 1406
  1433 - 1441
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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