Macromolecule-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 Macromolecule-Binding Periplasmic Protein
  Conformer 1
(PDB)
1kwh (A)
  Conformer 2
(PDB)
1j1n (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 267 0.52   134 - 310   401 - 490
2 221 0.35   3 - 133   311 - 400

Sequence


           ________________________________________________________________________________________________________________________ 
 1kwh(A) : KEATWVTDKPLTLKIHMHFRDKWVWDENWPVAKESFRLTNVKLQSVANKAATNSQEQFNLMMASGDLPDVVGGDNLKDKFIQYGQEGAFVPLNKLIDQYAPHIKAFFKSHPEVERAIKAP 
         :                                                                                                                          
 1j1n(B) : KEATWVTDKPLTLKIHMHFRDKWVWDENWPVAKESFRLTNVKLQSVANKAATNSQEQFNLMMASGDLPDVVGGDNLKDKFIQYGQEGAFVPLNKLIDQYAPHIKAFFKSHPEVERAIKAP 
           ________________________________________________________________________________________________________________________ 

           _________132____________________________________________________________________________________________________________ 
 1kwh(A) : DGNIYFIPYVPDGVVARGYFIREDWLKKLNLKPPQNIDELYTVLKAFKEKDPNGNGKADEVPFIDRHPDEVFRLVNFWGARSSGSDNYMDFYIDNGRVKHPWAETAFRDGMKHVAQWYKE 
         :                                                                                                                          
 1j1n(B) : DGNIYFIPYVPDGVVARGYFIREDWLKKLNLKPPQNIDELYTVLKAFKEKDPNGNGKADEVPFIDRHPDEVFRLVNFWGARSSGSDNYMDFYIDNGRVKHPWAETAFRDGMKHVAQWYKE 
           _________132____________________________________________________________________________________________________________ 

           _________________________________________________________________308____________________________________________________ 
 1kwh(A) : GLIDKEIFTRKAKAREQMFGGNLGGFTHDWFASTMTFNEGLAKTVPGFKLIPIAPPTNSKGQRWEEDSRQKVRPDGWAITVKNKNPVETIKFFDFYFSRPGRDISNFGVPGVTYDIKNGK 
         :                                                                                                                          
 1j1n(B) : GLIDKEIFTRKAKAREQMFGGNLGGFTHDWFASTMTFNEGLAKTVPGFKLIPIAPPTNSKGQRWEEDSRQKVRPDGWAITVKNKNPVETIKFFDFYFSRPGRDISNFGVPGVTYDIKNGK 
           _________________________________________________________________308____________________________________________________ 

           ___________________________________398__________________________________________________________________________________ 
 1kwh(A) : AVFKDSVLKSPQPVNNQLYDMGAQIPIGFWQDYDYERQWTTPEAQAGIDMYVKGKYVMPGFEGVNMTREERAIYDKYWADVRTYMYEMGQAWVMGTKDVDKTWDEYQRQLKLRGLYQVLQ 
         :                                                                                                                          
 1j1n(B) : AVFKDSVLKSPQPVNNQLYDMGAQIPIGFWQDYDYERQWTTPEAQAGIDMYVKGKYVMPGFEGVNMTREERAIYDKYWADVRTYMYEMGQAWVMGTKDVDKTWDEYQRQLKLRGLYQVLQ 
           ___________________________________398__________________________________________________________________________________ 

           ____________                                                                                                             
 1kwh(A) : MMQQAYDRQYKN                                                                                                             
         :                                                                                                                          
 1j1n(B) : MMQQAYDRQYKN                                                                                                             
           ____________                                                                                                             

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
29.7
Translation
(A)
0.4
Closure
(%)
99.5
Bending Residues
( green )
  132 - 136
  308 - 311
  398 - 401
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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