D-Xylose-Binding Periplasmic Protein

(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 D-Xylose-Binding Periplasmic Protein
  Conformer 1
(PDB)
3m9w (A)
  Conformer 2
(PDB)
3ma0 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 160 0.41   105 - 242   284 - 305
2 141 0.77   5 - 104   243 - 283

Sequence


           _____________________________________________________________________________________________________104________________ 
 3m9w(A) : **VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDI 
         :                                                                                                                          
 3ma0(A) : KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDI 
           _____________________________________________________________________________________________________104________________ 

           ______________________________________________________________________________________________________________________24 
 3m9w(A) : VPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTV 
         :                                                                                                                          
 3ma0(A) : VPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTV 
           ______________________________________________________________________________________________________________________24 

           1_____________________________________281________________________________                                                
 3m9w(A) : YKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL******                                                
         :                                                                                                                          
 3ma0(A) : YKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESELHHHHHH                                                
           1_____________________________________281________________________________                                                

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
32.7
Translation
(A)
-0.1
Closure
(%)
89.5
Bending Residues
( green )
  104 - 105
  241 - 243
  281 - 285
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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