Glutamate Receptor, Ionotropic Kainate 1

(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 Glutamate Receptor, Ionotropic Kainate 1
  Conformer 1
(PDB)
3s2v (B)
  Conformer 2
(PDB)
4mf3 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 145 0.69   6 - 109   212 - 252
2 85 0.52   110 - 110   113 - 186   190 - 190   194 - 196   206 - 211
3 20 0.63   111 - 112   187 - 189   191 - 193   197 - 205   253 - 255

Sequence


           ___________________________________________________________________________________________________________109__________ 
 3s2v(B) : *GANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTP 
         :                                                                                                                          
 4mf3(A) : SLANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFIYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTP 
           ___________________________________________________________________________________________________________110__________ 

           ________________________________________________________________186____193_________205_209______________________________ 
 3s2v(B) : IDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQE 
         :                                                                                                                          
 4mf3(A) : IDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQTALVRNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQE 
           ________________________________________________________________187____194_________206_210______________________________ 

           ________250_______                                                                                                       
 3s2v(B) : EGKLHMMKEKWWRGNGCP                                                                                                       
         :                                                                                                                          
 4mf3(A) : EGKLHMMKEKWWRGNGCP                                                                                                       
           ________251_______                                                                                                       

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 11.1 0.2 82.2   109 - 110   209 - 213 Bending Region Analysis
1 3 15.4 -0.3 66.5   109 - 111   250 - 255 Bending Region Analysis
2 3 9.4 0.1 100.0   110 - 113   186 - 187   189 - 191   193 - 194   196 - 197   205 - 206 Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 2 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 2

Movement classification: Hinge

PyMOL Script

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