DNA 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 DNA Polymerase
  Conformer 1
(PDB)
2gv9 (B)
  Conformer 2
(PDB)
2gv9 (A)
  Window Length 9
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 689 1.39   64 - 703   723 - 847
2 278 1.53   704 - 722   848 - 1193

Sequence


           ________________________________________________________________________________________________________________________ 
 2gv9(B) : TGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCGGDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAYGMRAAQFHARFMDAITPT 
         :                                                                                                                          
 2gv9(A) : *GPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCGGDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAYGMRAAQFHARFMDAITPT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2gv9(B) : GTVITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRES-----rGISADHFEAEVVERTDVYYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVD 
         :                                                                                                                          
 2gv9(A) : GTVITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDVYYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2gv9(B) : ATTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEHVLLFSLGSCD 
         :                                                                                                                          
 2gv9(A) : ATTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEHVLLFSLGSCD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2gv9(B) : LPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQKRSKIKVNGMVNIDMYGIITDKIKLSSY 
         :                                                                                                                          
 2gv9(A) : LPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWD----------kIKVNGMVNIDMYGIITDKIKLSSY 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________________________________________________703_______________ 
 2gv9(B) : KLNAVAEAVLKDKKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDT-vLDPTSGFHVNPVVVFDF 
         :                                                                                                                          
 2gv9(A) : KLNAVAEAVLKDKKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQvLDPTSGFHVNPVVVFDF 
           ______________________________________________________________________________________________________703_______________ 

           _722____________________________________________________________________________________________________________________ 
 2gv9(B) : ASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVT 
         :                                                                                                                          
 2gv9(A) : ASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVT 
           _722____________________________________________________________________________________________________________________ 

           ______847_______________________________________________________________________________________________________________ 
 2gv9(B) : TIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLV 
         :                                                                                                                          
 2gv9(A) : TIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLV 
           ______847_______________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2gv9(B) : RKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQVPSIKDRIPYVIVA 
         :                                                                                                                          
 2gv9(A) : RKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDPERDIQDFVLTA-------------------------------sIKDRIPYVIVA 
           ________________________________________________________________________________________________________________________ 

           _________________________________________________________________________________                                        
 2gv9(B) : QTREVEETVARLAALRELDkLLVSELAEDPAYAIAHGVALNTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIPEVWH                                        
         :                                                                                                                          
 2gv9(A) : Q------------------kLLVSELAEDPAYAIAHGVALNTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIPEVWH                                        
           _________________________________________________________________________________                                        

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)
7.4
Translation
(A)
-2.0
Closure
(%)
44.3
Bending Residues
( green )
  703 - 704
  722 - 723
  847 - 848
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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