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)	6l6f (A)
Window Length	11
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	133	1.25	10 - 107 215 - 249
2	110	2.02	108 - 214 250 - 253

Sequence

`________________________________________________________________________________________________________________________` `2f36(A) : **********************************************************************************************************************` `:` `6l6f(A) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6l6f(A) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `6l6f(A) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERgVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________107_____` `2f36(A) : ********TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISI` `:` `6l6f(A) : VWSPADGLNInRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSI` `________________________________________________________________________________________________________________506_____` `________________________________________________________________________________________________________________________` `2f36(A) : LYRK--GT-----------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWA` `:` `6l6f(A) : LYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARlSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWA` `________________________________________________________________________________________________________________________` `__________________________________________________212__________________________________249__________________________` `2f36(A) : FMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPS***************` `:` `6l6f(A) : FMSSKP-SALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `__________________________________________________730__________________________________767__________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	20.1
Translation (A)	1.7
Closure (%)	95.3
Bending Residues ( green )	107 - 108 212 - 215 249 - 251
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

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