Large Fragment Of DNA Polymerase I

(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 Large Fragment Of DNA Polymerase I
  Conformer 1
(PDB)
3ktq (A)
  Conformer 2
(PDB)
5ktq (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 422 1.14   297 - 464   541 - 636   672 - 829
2 67 2.26   465 - 540
3 34 1.56   637 - 670

Sequence


           ________________________________________________________________________________________________________________________ 
 3ktq(A) : ***ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALS 
         :                                                                                                                          
 5ktq(A) : SPKALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________452_____________________________________________________________________________ 
 3ktq(A) : ERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIV 
         :                                                                                                                          
 5ktq(A) : ERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAI---------sTSAAVLEALREAHPIV 
           ________________________________________452_____________________________________________________________________________ 

           ________540________________________________________________________________________________________631__________________ 
 3ktq(A) : EKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 
         :                                                                                                                          
 5ktq(A) : EKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGV 
           ________540________________________________________________________________________________________631__________________ 

           __________________670___________________________________________________________________________________________________ 
 3ktq(A) : PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLF 
         :                                                                                                                          
 5ktq(A) : PREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLF 
           __________________670___________________________________________________________________________________________________ 

           _______________________________________________________________                                                          
 3ktq(A) : PRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK*                                                          
         :                                                                                                                          
 5ktq(A) : PRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE                                                          
           _______________________________________________________________                                                          

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)
28.9
Translation
(A)
0.0
Closure
(%)
57.3
Bending Residues
( green )
  452 - 465
  540 - 543
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
58.3
Translation
(A)
-1.8
Closure
(%)
86.3
Bending Residues
( green )
  631 - 637
  670 - 675
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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