Putrescine-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 Putrescine-Binding Periplasmic Protein
  Conformer 1
(PDB) 		6yed (A)
  Conformer 2
(PDB) 		1a99 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 171 0.93   136 - 276   338 - 367
2 166 0.81   31 - 135   277 - 337

Sequence


           ________________________________________________________________________________________________________135_____________ 
 6yed(A) : QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVK 
         :                                                                                                                          
 1a99(A) : QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVK 
           ________________________________________________________________________________________________________135_____________ 

           ________________________________________________________________________________________________________________________ 
 6yed(A) : AVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSI 
         :                                                                                                                          
 1a99(A) : AVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSI 
           ________________________________________________________________________________________________________________________ 

           ____275_________________________________________________327__________________________________________                    
 6yed(A) : PKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG                    
         :                                                                                                                          
 1a99(A) : PKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG                    
           ____275_________________________________________________327__________________________________________                    

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		40.7
Translation
(A) 		-1.0
Closure
(%) 		92.7
Bending Residues
( green ) 		  135 - 137
  275 - 277
  327 - 346
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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