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)
1y1z (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 166 0.62   7 - 144   247 - 287
2 102 0.8   145 - 246

Sequence


           ________________________________________________________________________________________________________________________ 
 4kcc(A) : STRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPN---hTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERV-----kEWNGMMGELLSGQADMIVAPLTI 
         :                                                                                                                          
 1y1z(A) : **RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNsPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTI 
           ________________________________________________________________________________________________________________________ 

           ______________144___________________________________________________________________________________________________246_ 
 4kcc(A) : NNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFR 
         :                                                                                                                          
 1y1z(A) : NNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFR 
           ______________144___________________________________________________________________________________________________246_ 

           ____________________________________________                                                                             
 4kcc(A) : SGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC*                                                                             
         :                                                                                                                          
 1y1z(A) : SGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECD                                                                             
           ____________________________________________                                                                             

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
24.4
Translation
(A)
-0.6
Closure
(%)
99.6
Bending Residues
( green )
  144 - 145
  246 - 248
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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