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

Domains

Domain Size Backbone RMSD
(A)
Residues
1 1007 1.02   22 - 1150
2 69 0.69   1151 - 1219

Sequence


           ________________________________________________________________________________________________________________________ 
 1i3q(B) : **DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLIeISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEkVFIGRLPIMLRSKNCY 
         :                                                                                                                          
 2nvy(B) : FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLIeISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEkVFIGRLPIMLRSKNCY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH 
         :                                                                                                                          
 2nvy(B) : LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIG---------kEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL 
         :                                                                                                                          
 2nvy(B) : ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : FKKLTKDIFRYMQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 
         :                                                                                                                          
 2nvy(B) : FKKLTKDIFRYMQRTVElAINAKTITSGLKYALATGNWGaGVSQVLNRYTYSSTLSHLRRTNTPIaKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEY 
         :                                                                                                                          
 2nvy(B) : EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDeYTWSSLLNEGLVEY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : IDAEEEESILIAMQPEDLEPdVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ 
         :                                                                                                                          
 2nvy(B) : IDAEEEESILIAMQPEDLEPdVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1i3q(B) : NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQVLV 
         :                                                                                                                          
 2nvy(B) : NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISsKRDASTPLRSTENGIVDQVLV 
           ________________________________________________________________________________________________________________________ 

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

           ________________________________________________________1150____________________________________________________________ 
 1i3q(B) : GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPgLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAM 
         :                                                                                                                          
 2nvy(B) : GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPgLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAM 
           ________________________________________________________1150____________________________________________________________ 

           ______________                                                                                                           
 1i3q(B) : NITPRLYTDRSRDF                                                                                                           
         :                                                                                                                          
 2nvy(B) : NITPRLYTDRSRDF                                                                                                           
           ______________                                                                                                           

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
12.9
Translation
(A)
-1.0
Closure
(%)
20.6
Bending Residues
( green )
  1150 - 1156
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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