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)
1i50 (B)
  Conformer 2
(PDB)
1i6h (B)
  Window Length 7
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 22 0.3   1130 - 1151
2 973 0.82   23 - 1106
3 70 1.48   1152 - 1221

Sequence


           ________________________________________________________________________________________________________________________ 
 1i50(B) : FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLIeISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEkVFIGRLPIMLRSKNCY 
         :                                                                                                                          
 1i6h(B) : **DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLI-iSFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKK----kVFIGRLPIMLRSKNCY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH 
         :                                                                                                                          
 1i6h(B) : LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL 
         :                                                                                                                          
 1i6h(B) : ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIG---------kEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : FKKLTKDIFRYMQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 
         :                                                                                                                          
 1i6h(B) : FKKLTKDIFRYMQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEY 
         :                                                                                                                          
 1i6h(B) : EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : IDAEEEESILIAMQPEDLEP---dVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELP 
         :                                                                                                                          
 1i6h(B) : IDAEEEESILIAMQPEDLEPAEAdVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : AGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQ 
         :                                                                                                                          
 1i6h(B) : AGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i50(B) : VLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEV 
         :                                                                                                                          
 1i6h(B) : VLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEV 
           ________________________________________________________________________________________________________________________ 

           _______________________________1106________________________________________1150_________________________________________ 
 1i50(B) : MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGP----------------gLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDI 
         :                                                                                                                          
 1i6h(B) : MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDI 
           _______________________________1106________________________________________1150_________________________________________ 

           _________________________________                                                                                        
 1i50(B) : YQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF                                                                                        
         :                                                                                                                          
 1i6h(B) : YQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF                                                                                        
           _________________________________                                                                                        

Morph

Morph animation in progress.
Status: Initialising

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.


Show console


play backwards pause play forwards

Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
2.1
Translation
(A)
1.1
Closure
(%)
74.1
Bending Residues
( green )
  1106 - 1131
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
28.2
Translation
(A)
0.3
Closure
(%)
90.3
Bending Residues
( green )
  1150 - 1157
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

Download and extract PyMOL PML script file Download