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)
1k83 (A)
  Conformer 2
(PDB)
1i3q (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1041 0.88   345 - 1397   1420 - 1428   1434 - 1443
2 316 0.88   7 - 336   1398 - 1419   1429 - 1433

Sequence


           ________________________________________________________________________________________________________________________ 
 1k83(A) : ***QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPE---------kIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
         :                                                                                                                          
 1i3q(A) : VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKK--------ePELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPV 
         :                                                                                                                          
 1i3q(A) : MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPV 
           ________________________________________________________________________________________________________________________ 

           ____________________________________________________________________________________________336_________________________ 
 1k83(A) : PPPPVR------------dDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQ------------sIRARLKGKEGRI--------vDFSARTVISGDPNLEL 
         :                                                                                                                          
 1i3q(A) : PPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL 
           ____________________________________________________________________________________________336_________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD 
         :                                                                                                                          
 1i3q(A) : DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK 
         :                                                                                                                          
 1i3q(A) : FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF 
         :                                                                                                                          
 1i3q(A) : DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL 
         :                                                                                                                          
 1i3q(A) : LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR 
         :                                                                                                                          
 1i3q(A) : VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL 
         :                                                                                                                          
 1i3q(A) : RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : kKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS-qQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK 
         :                                                                                                                          
 1i3q(A) : kKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLqQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1k83(A) : NDLFVIWSEDNDEKLIIRCRVVaEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKE 
         :                                                                                                                          
 1i3q(A) : NDLFVIWSEDNDEKLIIRCRVVaEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKE 
           ________________________________________________________________________________________________________________________ 

           __________________________________________1397__________________1419__________1433_________________                      
 1k83(A) : VYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESL                      
         :                                                                                                                          
 1i3q(A) : VYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI*****                      
           __________________________________________1397__________________1419__________1433_________________                      

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
13.6
Translation
(A)
0.4
Closure
(%)
72.9
Bending Residues
( green )
  336 - 345
  1397 - 1398
  1419 - 1429
  1433 - 1434
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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