Abc Transporter, Periplasmic Substrate-Binding 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 Abc Transporter, Periplasmic Substrate-Binding Protein
  Conformer 1
(PDB)
6jal (A)
  Conformer 2
(PDB)
6jam (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 218 0.39   118 - 285   354 - 403
2 183 1.23   3 - 117   286 - 353

Sequence


           ________________________________________________________________________________________________________________________ 
 6jal(A) : VPRGSHMMQSGPVIRVAGDSTAVGEGGRWMKEMVEAWGKKTGTRVEYIDSPADTNDRLALYQQYWAARSPDVDVYMIDVIWPGIVAPHALDLKPYLTEAELKEFFPRIVQNNTIRGKLTS 
         :                                                                                                                          
 6jam(A) : ********QSGPVIRVAGDSTAVGEGGRWMKEMVEAWGKKTGTRVEYIDSPADTNDRLALYQQYWAARSPDVDVYMIDVIWPGIVAPHALDLKPYLTEAELKEFFPRIVQNNTIRGKLTS 
           ________________________________________________________________________________________________________________________ 

           __117___________________________________________________________________________________________________________________ 
 6jal(A) : LPFFTDAGILYYRKDLLEKYGYTSPPRTWNELEQMAERVMEGERRAGNRDFWGFVFQGKPYEGLTCDALEWIYSHGGGRIVEPDGTISVNNGRAALALNRAHGWVGRIAPQGVTSYAEEE 
         :                                                                                                                          
 6jam(A) : LPFFTDAGILYYRKDLLEKYGYTSPPRTWNELEQMAERVMEGERRAGNRDFWGFVFQGKPYEGLTCDALEWIYSHGGGRIVEPDGTISVNNGRAALALNRAHGWVGRIAPQGVTSYAEEE 
           __117___________________________________________________________________________________________________________________ 

           _________________________________________________284__________________________________________________________________35 
 6jal(A) : ARNVWQQGNSLFMRNWPYAYALGQAEGSPIRGKFGVTVLPKASADAPNAATLGGWQLMVSAYSRYPKEAVDLVKYLASYEVQKDNAVRLSRLPTRPALYTDRDVLARNPWFRDLLPVFQN 
         :                                                                                                                          
 6jam(A) : ARNVWQQGNSLFMRNWPYAYALGQAEGSPIRGKFGVTVLPKASADAPNAATLGGWQLMVSAYSRYPKEAVDLVKYLASYEVQKDNAVRLSRLPTRPALYTDRDVLARNPWFRDLLPVFQN 
           _________________________________________________284__________________________________________________________________35 

           3_______________________________________________________                                                                 
 6jal(A) : AVSAPSDVAGARYNQVSEAIWTEVHSVLTGRKKGEQAVRDLEARIRRILRHHHHHH                                                                 
         :                                                                                                                          
 6jam(A) : AVSAPSDVAGARYNQVSEAIWTEVHSVLTGRKKGEQAVRDLEARIRRILRHHHH**                                                                 
           3_______________________________________________________                                                                 

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
41.8
Translation
(A)
-1.3
Closure
(%)
100.0
Bending Residues
( green )
  117 - 120
  284 - 286
  353 - 354
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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