Periplasmic 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 Periplasmic Binding Protein
  Conformer 1
(PDB) 		5l9p (A)
  Conformer 2
(PDB) 		5l9l (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 173 0.91   129 - 259   309 - 350
2 146 0.48   32 - 128   260 - 308

Sequence


           ________________________________________________________________________________________________________________127_____ 
 5l9p(A) : SHHHHHHSSGLVPRGSHMDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVESGSVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANSNYST 
         :                                                                                                                          
 5l9l(A) : *****************MDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVESGSVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANSNYST 
           ________________________________________________________________________________________________________________127_____ 

           ________________________________________________________________________________________________________________________ 
 5l9p(A) : LIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALALGTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGEVDMIITWGGRVQGAINDGANFAYT 
         :                                                                                                                          
 5l9l(A) : LIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALALGTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGEVDMIITWGGRVQGAINDGANFAYT 
           ________________________________________________________________________________________________________________________ 

           ___258___________________________________________304________________________________________________                     
 5l9p(A) : FNDAQLGTDGYAIVKGAPHRDAAMRFLKEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQYSVDPNFWAKHAKWASEAYDNVRL                     
         :                                                                                                                          
 5l9l(A) : FNDAQLGTDGYAIVKGAPHRDAAMRFLKEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQYSVDPNFWAKHAKWASEAYDNVRL                     
           ___258___________________________________________304________________________________________________                     

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		38.7
Translation
(A) 		-0.2
Closure
(%) 		99.5
Bending Residues
( green ) 		  127 - 130
  258 - 261
  304 - 320
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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