Endonuclease VIII

(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 Endonuclease VIII
  Conformer 1
(PDB)
1k3x (A)
  Conformer 2
(PDB)
1q3b (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 123 1.22   126 - 260
2 123 0.91   3 - 125

Sequence


           _______________________________________________________________________________________________________________________1 
 1k3x(A) : PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHP 
         :                                                                                                                          
 1q3b(A) : PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHP 
           _______________________________________________________________________________________________________________________1 

           22______________________________________________________________________________________________________________________ 
 1k3x(A) : FLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRG---------aLFRFKVFHRDGEPCERC 
         :                                                                                                                          
 1q3b(A) : FLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC 
           22______________________________________________________________________________________________________________________ 

           ______________________                                                                                                   
 1k3x(A) : GSIIEKTTLSSRPFYWCPGCQH                                                                                                   
         :                                                                                                                          
 1q3b(A) : GSIIEKTTL---pFYWCPGCQH                                                                                                   
           ______________________                                                                                                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
84.5
Translation
(A)
-2.3
Closure
(%)
99.9
Bending Residues
( green )
  122 - 126
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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