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)
1wcm (B)
  Window Length 11
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 971 0.91   25 - 1106
2 96 3.61   1107 - 1218

Sequence


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

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

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

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

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

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

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

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

           _____________________________1104_______________________________________________________________________________________ 
 1i50(B) : MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGP----------------gLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDI 
         :                                                                                                                          
 1wcm(B) : MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDI 
           _____________________________1104_______________________________________________________________________________________ 

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

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)
19.4
Translation
(A)
0.2
Closure
(%)
98.9
Bending Residues
( green )
  1104 - 1107
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

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