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)
2nvz (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 24 0.61   1129 - 1152
2 966 0.9   22 - 1106
3 69 1.56   1153 - 1221

Sequence


           ________________________________________________________________________________________________________________________ 
 1i3q(B) : DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLIeISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEkVFIGRLPIMLRSKNCYLS 
         :                                                                                                                          
 2nvz(B) : DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLI-iSFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDV------kVFIGRLPIMLRSKNCYLS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : EATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC 
         :                                                                                                                          
 2nvz(B) : EATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGS--iSTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGkEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY 
         :                                                                                                                          
 2nvz(B) : YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGkEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : MQRTVElAINAKTITSGLKYALATGNWG---------aGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEP 
         :                                                                                                                          
 2nvz(B) : MQRTVElAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : LEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEYID 
         :                                                                                                                          
 2nvz(B) : LEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEYID 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : AEEEESILIAMQPEDLEP--dVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ 
         :                                                                                                                          
 2nvz(B) : AEEEESILIAMQPEDLEPAEdVDPAKRIRVS--aTTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQVLV 
         :                                                                                                                          
 2nvz(B) : NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPIS--rDASTPLRSTENGIVDQVLV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYN 
         :                                                                                                                          
 2nvz(B) : TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYN 
           ________________________________________________________________________________________________________________________ 

           ____________________________1106_________________________________________1151___________________________________________ 
 1i3q(B) : GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGP----------------gLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQI 
         :                                                                                                                          
 2nvz(B) : GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQI 
           ____________________________1106_________________________________________1151___________________________________________ 

           ______________________________                                                                                           
 1i3q(B) : HIPYAAKLLFQELMAMNITPRLYTDRSRDF                                                                                           
         :                                                                                                                          
 2nvz(B) : HIPYAAKLLFQELMAMNITPRLYTDRSRD*                                                                                           
           ______________________________                                                                                           

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)
2.0
Translation
(A)
-0.1
Closure
(%)
91.4
Bending Residues
( green )
  1106 - 1129
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
36.1
Translation
(A)
1.3
Closure
(%)
80.5
Bending Residues
( green )
  1151 - 1158
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

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