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 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	144	1.22	7 - 107 191 - 194 215 - 253
2	102	1.91	108 - 190 195 - 214

Sequence

`________________________________________________________________________________________________________________________` `2f36(A) : **********************************************************************************************************************` `:` `6jfz(B) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(B) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(B) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERdGVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKV` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________________________________107___` `2f36(A) : **********TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGI` `:` `6jfz(B) : GVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGV` `__________________________________________________________________________________________________________________506___` `________________________________________________________________________________________________________________________` `2f36(A) : SILYRK--GT--------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAF` `:` `6jfz(B) : SILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVEpIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAF` `________________________________________________________________________________________________________________________` `___________________________190_194________________213______________________________________________________________` `2f36(A) : MSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPS***************` `:` `6jfz(B) : MSSKp-SALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `___________________________708_712________________731______________________________________________________________`

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)	26.1
Translation (A)	1.1
Closure (%)	100.0
Bending Residues ( green )	107 - 108 190 - 191 194 - 195 213 - 215
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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