Glutamate [Nmda] Receptor Subunit Zeta 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 [Nmda] Receptor Subunit Zeta 1
  Conformer 1
(PDB)
1y1m (A)
  Conformer 2
(PDB)
1pbq (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 161 0.88   7 - 143   248 - 283
2 104 0.5   144 - 247

Sequence


           ________________________________________________________________________________________________________________________ 
 1y1m(A) : RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPtVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQY 
         :                                                                                                                          
 1pbq(A) : RLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTG--vPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQY 
           ________________________________________________________________________________________________________________________ 

           ______143__________________________________________________________________________________________________244__________ 
 1y1m(A) : IEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGM 
         :                                                                                                                          
 1pbq(A) : IEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGM 
           ______143__________________________________________________________________________________________________244__________ 

           ____________________________________                                                                                     
 1y1m(A) : RKDSPWKQNVSLSILKSHENGFMEDLDKTWV*****                                                                                     
         :                                                                                                                          
 1pbq(A) : RKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC                                                                                     
           ____________________________________                                                                                     

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
8.3
Translation
(A)
0.7
Closure
(%)
55.6
Bending Residues
( green )
  143 - 146
  244 - 248
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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