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) 		8y5i (E)
  Conformer 2
(PDB) 		1pot (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 168 1.33   130 - 255   304 - 345
2 149 1.63   29 - 129   256 - 303

Sequence


           _____________________________________________________________________________________________________129________________ 
 8y5i(E) : *NTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDP 
         :                                                                                                                          
 1pot(A) : NNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDP 
           _____________________________________________________________________________________________________129________________ 

           ___________________________________________________________________________________________________________255__________ 
 8y5i(E) : KSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANA 
         :                                                                                                                          
 1pot(A) : KSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANA 
           ___________________________________________________________________________________________________________255__________ 

           ___________________________________303____________________________________________                                       
 8y5i(E) : KNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAG                                       
         :                                                                                                                          
 1pot(A) : KNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAG                                       
           ___________________________________303____________________________________________                                       

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		24.2
Translation
(A) 		-1.0
Closure
(%) 		97.3
Bending Residues
( green ) 		  129 - 130
  255 - 256
  303 - 304
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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