Glutamate Receptor Ionotropic, Nmda 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, Nmda 1
  Conformer 1
(PDB)
4kcc (A)
  Conformer 2
(PDB)
1pbq (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 156 0.63   7 - 143   248 - 283
2 109 0.78   144 - 247   284 - 288

Sequence


           ________________________________________________________________________________________________________________________ 
 4kcc(A) : STRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNhTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERV-----kEWNGMMGELLSGQADMIVAPLTINNE 
         :                                                                                                                          
 1pbq(A) : **RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTG----vPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNE 
           ________________________________________________________________________________________________________________________ 

           _________142___________________________________________________________________________________________________244______ 
 4kcc(A) : RAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGF 
         :                                                                                                                          
 1pbq(A) : RAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGF 
           _________142___________________________________________________________________________________________________244______ 

           ______________________________283_______                                                                                 
 4kcc(A) : GIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC                                                                                 
         :                                                                                                                          
 1pbq(A) : GIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC                                                                                 
           ______________________________283_______                                                                                 

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
9.6
Translation
(A)
0.6
Closure
(%)
2.6
Bending Residues
( green )
  142 - 146
  244 - 248
  283 - 284
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Mixed

PyMOL Script

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