DynDom - Protein Domain Motions

Glutamate Receptor, Ionotropic Kainate 2

(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 2
Conformer 1 (PDB)	4mh5 (A)
Conformer 2 (PDB)	6jfz (D)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	127	1.33	6 - 96 204 - 239
2	111	3.56	97 - 203 240 - 243

Sequence

`________________________________________________________________________________________________________________________` `4mh5(A) : **********************************************************************************************************************` `:` `6jfz(D) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4mh5(A) : ********************************************************************************************************************` `:` `6jfz(D) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4mh5(A) : ********************************************************************************************************************` `:` `6jfz(D) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERLQgVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEK` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________________96___` `4mh5(A) : *******************GTNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREK` `:` `6jfz(D) : VGVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLG` `__________________________________________________________________________________________________________________505___` `________________________________________________________________________________________________________________________` `4mh5(A) : AIDFSKP--FM------------------------------------------------------------------------TLGVSILYRKGTPIDSADDLAKQTKIEYGAVKDGATM` `:` `6jfz(D) : VSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFE` `________________________________________________________________________________________________________________________` `______________________________________________________202__________________________________239_________________________` `4mh5(A) : TFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCP****` `:` `6jfz(D) : KMWAFMSSKpSALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `______________________________________________________731__________________________________768_________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	24.9
Translation (A)	1.2
Closure (%)	99.7
Bending Residues ( green )	96 - 99 202 - 204 239 - 243
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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