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)
1ryr (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 172 1.17   3 - 173   227 - 231   236 - 237
2 57 0.95   174 - 226   232 - 235
3 99 0.66   241 - 339

Sequence


           ________________________________________________________________________________________________________________________ 
 2rdi(A) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFsG------AVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
         :                                                                                                                          
 1ryr(A) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
           ________________________________________________________________________________________________________________________ 

           __________________________________________________173__________________________________________________226__231__236____ 
 2rdi(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
         :                                                                                                                          
 1ryr(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
           __________________________________________________173__________________________________________________226__231__236____ 

           ______________________________________________________________________________________________________                   
 2rdi(A) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIT                   
         :                                                                                                                          
 1ryr(A) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI*                   
           ______________________________________________________________________________________________________                   

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.


Show console


play backwards pause play forwards

Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
11.8
Translation
(A)
-0.1
Closure
(%)
99.6
Bending Residues
( green )
  173 - 174
  226 - 227
  231 - 237
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
133.8
Translation
(A)
-1.0
Closure
(%)
26.7
Bending Residues
( green )
  236 - 244
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

Download and extract PyMOL PML script file Download