Bacteriophage T7 RNA Polymerase

(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 Bacteriophage T7 RNA Polymerase
  Conformer 1
(PDB)
1qln (A)
  Conformer 2
(PDB)
1msw (D)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 663 5.28   8 - 73   258 - 881
2 136 1.99   74 - 163   204 - 257

Sequence


           _________________________________________44_____________________________________________________________________________ 
 1qln(A) : ****IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF----------------pLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT 
         :                                                                                                                          
 1msw(D) : NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT 
           _________________________________________44_____________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1qln(A) : TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDS 
         :                                                                                                                          
 1msw(D) : TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQ--------s 
           ________________________________________________________________________________________________________________________ 

           ____________256_________________________________________________________________________________________________________ 
 1qln(A) : ETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP 
         :                                                                                                                          
 1msw(D) : ETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP 
           ____________256_________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1qln(A) : MKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF 
         :                                                                                                                          
 1msw(D) : MK-----------tAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1qln(A) : IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN 
         :                                                                                                                          
 1msw(D) : IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1qln(A) : TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK 
         :                                                                                                                          
 1msw(D) : TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1qln(A) : RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV 
         :                                                                                                                          
 1msw(D) : RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV 
           ________________________________________________________________________________________________________________________ 

           __________________________________________                                                                               
 1qln(A) : LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA                                                                               
         :                                                                                                                          
 1msw(D) : LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA                                                                               
           __________________________________________                                                                               

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
135.0
Translation
(A)
-23.1
Closure
(%)
53.2
Bending Residues
( green )
  44 - 75
  256 - 268
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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