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) 		5l9g (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 174 1.04   129 - 259   308 - 350
2 145 0.46   32 - 128   260 - 307

Sequence


           _________________________________________________________________________________________________________________128____ 
 5l9p(A) : SHHHHHHSSGLVPRGSHMDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVESGSVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANSNYST 
         :                                                                                                                          
 5l9g(A) : *****************MDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVESGSVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANSNYST 
           _________________________________________________________________________________________________________________128____ 

           ________________________________________________________________________________________________________________________ 
 5l9p(A) : LIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALALGTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGEVDMIITWGGRVQGAINDGANFAYT 
         :                                                                                                                          
 5l9g(A) : LIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALALGTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGEVDMIITWGGRVQGAINDGANFAYT 
           ________________________________________________________________________________________________________________________ 

           ___258__________________________________________303___________________________________________________                   
 5l9p(A) : FNDAQLGTDGYAIVKGAPHRDAAMRFLKEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQYSVDPNFWAKHAKWASEAYDNVRL**                   
         :                                                                                                                          
 5l9g(A) : FNDAQLGTDGYAIVKGAPHRDAAMRFLKEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQYSVDPNFWAKHAKWASEAYDNVRLSR                   
           ___258__________________________________________303___________________________________________________                   

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		39.0
Translation
(A) 		-0.5
Closure
(%) 		99.0
Bending Residues
( green ) 		  128 - 130
  258 - 261
  303 - 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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