DNA Polymerase IV (Family Y)

(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 IV (Family Y)
  Conformer 1
(PDB) 		2rdi (A)
  Conformer 2
(PDB) 		3v6j (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 166 1.17   3 - 167   177 - 178   232 - 236
2 62 0.67   168 - 176   179 - 231
3 100 0.66   241 - 340

Sequence


           ________________________________________________________________________________________________________________________ 
 2rdi(A) : *MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFsG------AVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYR 
         :                                                                                                                          
 3v6j(A) : HMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYR 
           ________________________________________________________________________________________________________________________ 

           _____________________________________________167______176____________________________________________________231__236___ 
 2rdi(A) : EAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRT 
         :                                                                                                                          
 3v6j(A) : EAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRT 
           _____________________________________________167______176____________________________________________________231__236___ 

           _______________________________________________________________________________________________________                  
 2rdi(A) : RVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIT                  
         :                                                                                                                          
 3v6j(A) : RVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE                  
           _______________________________________________________________________________________________________                  

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		12.6
Translation
(A) 		-0.4
Closure
(%) 		100.0
Bending Residues
( green ) 		  167 - 168
  176 - 179
  231 - 232
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( yellow ) 		3
Rotation Angle
(deg) 		136.3
Translation
(A) 		0.3
Closure
(%) 		33.8
Bending Residues
( green ) 		  236 - 243
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

PyMOL Script

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