DynDom - Protein Domain Motions

Glutamate Receptor, Ionotropic Kainate 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 Kainate 1
Conformer 1 (PDB)	2f36 (A)
Conformer 2 (PDB)	6jfz (C)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	139	1.08	7 - 107 215 - 252
2	109	3.87	108 - 214 253 - 255

Sequence

`________________________________________________________________________________________________________________________` `2f36(A) : **********************************************************************************************************************` `:` `6jfz(C) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(C) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(C) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERdGVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKV` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________________________106____` `2f36(A) : **********TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGI` `:` `6jfz(C) : GVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGV` `_________________________________________________________________________________________________________________505____` `________________________________________________________________________________________________________________________` `2f36(A) : SILYRK--GT------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEK` `:` `6jfz(C) : SILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEK` `________________________________________________________________________________________________________________________` `_______________________________________________________214___________________________________252_______________________` `2f36(A) : MWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPS***************` `:` `6jfz(C) : MWAFMSSKp-SALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `_______________________________________________________732___________________________________770_______________________`

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)	23.7
Translation (A)	2.4
Closure (%)	99.6
Bending Residues ( green )	106 - 108 214 - 215 252 - 253
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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