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 DNA Polymerase I
  Conformer 1
(PDB)
3hp6 (A)
  Conformer 2
(PDB)
1lv5 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 543 0.7   299 - 678   711 - 874
2 32 0.61   679 - 710

Sequence


           ________________________________________________________________________________________________________________________ 
 3hp6(A) : AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIEL-gVSFDLLLAAYLLDPAQGVDDVAAAAKM 
         :                                                                                                                          
 1lv5(A) : AKMAFTLADRVTEEMLADKAALVVEVVEENYHAAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKM 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 3hp6(A) : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV 
         :                                                                                                                          
 1lv5(A) : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 3hp6(A) : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ 
         :                                                                                                                          
 1lv5(A) : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ 
           ________________________________________________________________________________________________________________________ 

           __________________677______________________________710__________________________________________________________________ 
 3hp6(A) : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI 
         :                                                                                                                          
 1lv5(A) : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI 
           __________________677______________________________710__________________________________________________________________ 

           ____________________________________________________________________________________________________                     
 3hp6(A) : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK                     
         :                                                                                                                          
 1lv5(A) : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK                     
           ____________________________________________________________________________________________________                     

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
30.1
Translation
(A)
-1.0
Closure
(%)
75.2
Bending Residues
( green )
  677 - 679
  710 - 714
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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