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 (D)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	139	1.36	9 - 110 214 - 250
2	106	3.55	111 - 213 251 - 254

Sequence

`________________________________________________________________________________________________________________________` `2f36(A) : **********************************************************************************************************************` `:` `6jfz(D) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(D) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6jfz(D) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERLQgVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEK` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________108_` `2f36(A) : ***********TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLG` `:` `6jfz(D) : VGVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLG` `____________________________________________________________________________________________________________________507_` `________________________________________________________________________________________________________________________` `2f36(A) : ISILYRK--GT------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYE` `:` `6jfz(D) : VSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFE` `________________________________________________________________________________________________________________________` `_______________________________________________________213__________________________________250_________________________` `2f36(A) : KMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPS***************` `:` `6jfz(D) : KMWAFMSSKp-SALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `_______________________________________________________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)	24.1
Translation (A)	1.7
Closure (%)	100.0
Bending Residues ( green )	108 - 111 213 - 214 250 - 254
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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