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)
1jx4 (A)
  Conformer 2
(PDB)
1s0n (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 124 0.31   4 - 4   6 - 6   10 - 35   40 - 93   97 - 106   118 - 118   128 - 143   152 - 152   154 - 165   170 - 170   236 - 239
2 104 0.25   5 - 5   7 - 9   94 - 96   107 - 117   119 - 127   144 - 151   153 - 153   166 - 169   171 - 235
3 103 0.36   36 - 39   240 - 339

Sequence


           ___4____9________________________35__39____________________________________________________93_96_______106______115_____ 
 1jx4(A) : *IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLP-rKEVYQQVSSRI-nLLREYSEKIEIASIDEAYLDISDKVRDYRE 
         :                                                                                                                          
 1s0n(A) : MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYRE 
           ___4____9________________________35__39____________________________________________________93_96_______106______115_____ 

           ____127_____________143_____151___________165_169_______________________________________________________________235_239_ 
 1jx4(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAAD-aKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKG-iGEAKAKYLISLARDEYNEPIRTR 
         :                                                                                                                          
 1s0n(A) : AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR 
           ____127_____________143_____151___________165_169_______________________________________________________________235_239_ 

           _____________________________________________________________________________________________________                    
 1jx4(A) : VRKSIGRIVT-kRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI                    
         :                                                                                                                          
 1s0n(A) : VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI                    
           _____________________________________________________________________________________________________                    

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
2.5
Translation
(A)
0.2
Closure
(%)
69.3
Bending Residues
( green )
  4 - 7
  9 - 10
  93 - 94
  96 - 97
  106 - 107
  115 - 119
  127 - 128
  143 - 144
  151 - 154
  165 - 166
  169 - 171
  235 - 238
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
2.1
Translation
(A)
-0.2
Closure
(%)
90.8
Bending Residues
( green )
  35 - 37
  39 - 40
  239 - 240
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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