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)
1n48 (A)
  Conformer 2
(PDB)
2asd (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 123 0.64   4 - 4   6 - 6   9 - 91   96 - 99   106 - 111   118 - 121   123 - 141   237 - 241
2 116 0.58   3 - 3   5 - 5   7 - 8   92 - 95   100 - 105   112 - 117   122 - 122   142 - 236
3 97 0.42   243 - 339

Sequence


           __3______________________________________________________________________________________91__95__99___105___111___117_12 
 1n48(A) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
         :                                                                                                                          
 2asd(B) : GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
           _______________________________________________________________________________________1091____1099__1105__1111__1117___ 

           1_________________141____________________________________________________________________________________________236____ 
 1n48(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
         :                                                                                                                          
 2asd(B) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
           _________________1141___________________________________________________________________________________________1236____ 

           ______________________________________________________________________________________________________                   
 1n48(A) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE                   
         :                                                                                                                          
 2asd(B) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI*                   
           ______________________________________________________________________________________________________                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
6.4
Translation
(A)
0.2
Closure
(%)
83.7
Bending Residues
( green )
  3 - 9
  91 - 92
  95 - 96
  99 - 100
  105 - 106
  111 - 112
  117 - 118
  121 - 123
  141 - 142
  236 - 237
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
63.2
Translation
(A)
3.8
Closure
(%)
94.7
Bending Residues
( green )
  238 - 245
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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