T7 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 T7 DNA Polymerase
  Conformer 1
(PDB) 		2ajq (A)
  Conformer 2
(PDB) 		1t8e (A)
  Window Length 11
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 593 2.87   6 - 101   143 - 502   563 - 699
2 29 8.41   102 - 136
3 60 2.03   503 - 562

Sequence


           ______________________________________________________________________________________________96________________________ 
 2ajq(A) : MIVSAIAANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRF 
         :                                                                                                                          
 1t8e(A) : MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPG--- 
           ______________________________________________________________________________________________96________________________ 

           ___________134__________________________________________________________________________________________________________ 
 2ajq(A) : GSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIE 
         :                                                                                                                          
 1t8e(A) : ---ALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIE 
           ___________134__________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2ajq(A) : ELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKG 
         :                                                                                                                          
 1t8e(A) : ELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKG 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2ajq(A) : APVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLE 
         :                                                                                                                          
 1t8e(A) : APVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLE 
           ________________________________________________________________________________________________________________________ 

           ________________499__________________________________________________________560________________________________________ 
 2ajq(A) : LRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRK 
         :                                                                                                                          
 1t8e(A) : LRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRK 
           ________________499__________________________________________________________560________________________________________ 

           ________________________________________________________________________________________________________                 
 2ajq(A) : VHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH                 
         :                                                                                                                          
 1t8e(A) : VHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH                 
           ________________________________________________________________________________________________________                 

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		105.0
Translation
(A) 		3.3
Closure
(%) 		75.3
Bending Residues
( green ) 		  96 - 102
  134 - 146
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( yellow ) 		3
Rotation Angle
(deg) 		28.3
Translation
(A) 		1.8
Closure
(%) 		99.9
Bending Residues
( green ) 		  499 - 507
  560 - 576
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: Mixed

PyMOL Script

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