Glutamate Receptor Ionotropic, Nmda 2A

(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 2A
  Conformer 1
(PDB)
4nf5 (B)
  Conformer 2
(PDB)
4nf8 (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 179 1.0   9 - 135   141 - 143   223 - 231   237 - 282
2 89 0.78   136 - 140   144 - 222   232 - 236

Sequence


           ________________________________________________________________________________________________________________________ 
 4nf5(B) : **NHLSIVTLEEAPFVIVEDI------cVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEV 
         :                                                                                                                          
 4nf8(B) : DDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEV 
           ________________________________________________________________________________________________________________________ 

           ________135__140_______________________________________________________________________________222______231_____________ 
 4nf5(B) : VDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTG 
         :                                                                                                                          
 4nf8(B) : VDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTG 
           ________135__140_______________________________________________________________________________222______231_____________ 

           _________________________________________                                                                                
 4nf5(B) : YGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICH                                                                                
         :                                                                                                                          
 4nf8(B) : YGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC*                                                                                
           _________________________________________                                                                                

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
14.7
Translation
(A)
-0.2
Closure
(%)
96.4
Bending Residues
( green )
  135 - 136
  140 - 141
  143 - 146
  222 - 223
  231 - 240
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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