Dna-Directed RNA Polymerase II 140Kd Polypeptide

(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 140Kd Polypeptide
  Conformer 1
(PDB)
1i3q (B)
  Conformer 2
(PDB)
1i6h (B)
  Window Length 11
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 972 0.62   25 - 1107
2 96 3.58   1108 - 1219

Sequence


           ________________________________________________________________________________________________________________________ 
 1i3q(B) : DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLIeISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEkVFIGRLPIMLRSKNCYLS 
         :                                                                                                                          
 1i6h(B) : DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLI-iSFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKK----kVFIGRLPIMLRSKNCYLS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : EATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC 
         :                                                                                                                          
 1i6h(B) : EATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGkEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY 
         :                                                                                                                          
 1i6h(B) : YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGkEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : MQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQS 
         :                                                                                                                          
 1i6h(B) : MQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : PDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEYIDAEEEESILI 
         :                                                                                                                          
 1i6h(B) : PDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEYIDAEEEESILI 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : AMQPEDLEP---dVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIAC 
         :                                                                                                                          
 1i6h(B) : AMQPEDLEPAEAdVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIAC 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : YSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQVLVTTNQDGLK 
         :                                                                                                                          
 1i6h(B) : YSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQVLVTTNQDGLK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLM 
         :                                                                                                                          
 1i6h(B) : FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLM 
           ________________________________________________________________________________________________________________________ 

           __________________1104__________________________________________________________________________________________________ 
 1i3q(B) : AQIFFGPTYYQRLRHMVDDKIHARARGP----------------gLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKL 
         :                                                                                                                          
 1i6h(B) : AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKL 
           __________________1104__________________________________________________________________________________________________ 

           ______________________                                                                                                   
 1i3q(B) : LFQELMAMNITPRLYTDRSRDF                                                                                                   
         :                                                                                                                          
 1i6h(B) : LFQELMAMNITPRLYTDRSRDF                                                                                                   
           ______________________                                                                                                   

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)
25.7
Translation
(A)
-0.5
Closure
(%)
92.1
Bending Residues
( green )
  1104 - 1108
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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