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) 		1l3s (A)
  Conformer 2
(PDB) 		3hp6 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 516 0.87   299 - 680   740 - 874
2 36 0.91   681 - 716
3 23 0.47   717 - 739

Sequence


           ________________________________________________________________________________________________________________________ 
 1l3s(A) : AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKM 
         :                                                                                                                          
 3hp6(A) : AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIEL-gVSFDLLLAAYLLDPAQGVDDVAAAAKM 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1l3s(A) : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV 
         :                                                                                                                          
 3hp6(A) : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1l3s(A) : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ 
         :                                                                                                                          
 3hp6(A) : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ 
           ________________________________________________________________________________________________________________________ 

           _____________________680_________________________________716____________________739_____________________________________ 
 1l3s(A) : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI 
         :                                                                                                                          
 3hp6(A) : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI 
           _____________________680_________________________________716____________________739_____________________________________ 

           ____________________________________________________________________________________________________                     
 1l3s(A) : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK                     
         :                                                                                                                          
 3hp6(A) : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK                     
           ____________________________________________________________________________________________________                     

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 21.9 -0.4 58.8   680 - 681 Bending Region Analysis
1 3 18.3 -1.6 67.0   739 - 740 Bending Region Analysis
3 2 19.5 0.2 55.5   716 - 718 Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 3 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 3

Movement classification: Hinge

PyMOL Script

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