DNA Polymerase IV

(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
  Conformer 1
(PDB) 		2agp (B)
  Conformer 2
(PDB) 		2rdi (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 179 1.19   3 - 178   228 - 236
2 49 0.84   179 - 227
3 99 0.59   241 - 339

Sequence


           ________________________________________________________________________________________________________________________ 
 2agp(B) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
         :                                                                                                                          
 2rdi(A) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFsG------AVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
           ________________________________________________________________________________________________________________________ 

           _______________________________________________________178______________________________________________227______236____ 
 2agp(B) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
         :                                                                                                                          
 2rdi(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
           _______________________________________________________178______________________________________________227______236____ 

           ______________________________________________________________________________________________________                   
 2agp(B) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI*                   
         :                                                                                                                          
 2rdi(A) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIT                   
           ______________________________________________________________________________________________________                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		11.2
Translation
(A) 		-0.2
Closure
(%) 		87.5
Bending Residues
( green ) 		  178 - 179
  227 - 228
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( yellow ) 		3
Rotation Angle
(deg) 		133.4
Translation
(A) 		-1.3
Closure
(%) 		22.2
Bending Residues
( green ) 		  236 - 247
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Hinge

PyMOL Script

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