Cyclic Nucleotide Binding Domain

(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 Cyclic Nucleotide Binding Domain
  Conformer 1
(PDB)
1u12 (B)
  Conformer 2
(PDB)
1vp6 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 75 1.32   250 - 323   345 - 345
2 27 1.32   223 - 249
3 21 0.75   324 - 344

Sequence


           _____________________________249_______________________________________________________________________323______________ 
 1u12(B) : ***GDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEI 
         :                                                                                                                          
 1vp6(A) : VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEI 
           _____________________________249_______________________________________________________________________323______________ 

           ____344______                                                                                                            
 1u12(B) : AEIFRKTALE***                                                                                                            
         :                                                                                                                          
 1vp6(A) : AEIFRKTALERRG                                                                                                            
           ____344______                                                                                                            

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
40.7
Translation
(A)
-0.1
Closure
(%)
5.3
Bending Residues
( green )
  249 - 250
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
47.7
Translation
(A)
-0.4
Closure
(%)
99.9
Bending Residues
( green )
  323 - 324
  344 - 345
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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