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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	83	18.76	102 - 152 175 - 206
2	93	12.42	9 - 101
3	26	16.85	220 - 245

Sequence

`________________________________________________________________________________________________________________________` `4mh5(A) : ****************************************************************************GTNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKE` `:` `6jfz(B) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `______________________________________________________101_______________________________________________________________` `4mh5(A) : LAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTL--GV--------------------------------------------------` `:` `6jfz(B) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `______________________________________________________179_______________________________________________________________` `__________________________________________________________________________________________________________203___________` `4mh5(A) :` `------------------SILYRKGTPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDS` `:` `6jfz(B) :` `YSGVNLTGFRILNVDNPHVSAIVEKWSMERdGVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKV` `__________________________________________________________________________________________________________363___________` `________________________________________________________________________________________________________________________` `4mh5(A) : KGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCP************************************************************************` `:` `6jfz(B) : GVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4mh5(A) : ********************************************************************************************************************` `:` `6jfz(B) : SILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVEpIDSADDLAKQTKIEYGAVKDGATMTFF-KKSKISTFEKMWA` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________` `4mh5(A) : ******************************************************************************************************************` `:` `6jfz(B) : FMSSKpSALVKNNeEGIQRTLTADYALLME-STTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGqKIGGIFIVLAAGLVLSVLVAV` `____________________________________________________________________________________________________________________`

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)	125.1
Translation (A)	-3.0
Closure (%)	96.7
Bending Residues ( green )	101 - 102
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	93.6
Translation (A)	-57.7
Closure (%)	99.8
Bending Residues ( green )	203 - 220
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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