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)	5kuf (A)
Conformer 2 (PDB)	6jfz (A)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	503	2.64	7 - 503 732 - 765
2	102	1.19	504 - 513 639 - 731
3	101	2.34	514 - 638 766 - 804

Sequence

`________________________________________________________________________________________________________________________` `5kuf(A) : THVLRFGGIFEYVESGP----MGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVS` `:` `6jfz(A) : *HVIRIGGIFEYAD-GPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : LYPDFSSLSRAILDLVQFFKWKTVTVVYDDSTGLIRLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHEMAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEP` `:` `6jfz(A) : LYPDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : YRYSGVNMTGFRILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRTDFD` `:` `6jfz(A) : YRYSGVNLTGFRILNVDNPHVSAIVEKWSMERLQ-----------gVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : LDVISLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDH` `:` `6jfz(A) : LDIISLKEDGLEKVGVWSPADGLNIt---------------NRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDD-KGQWNGMVKELIDH` `________________________________________________________________________________________________________________________` `_______________________503_______513____________________________________________________________________________638_____` `5kuf(A) : KADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDL` `:` `6jfz(A) : KADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIAR-lSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDL` `_______________________505_______515____________________________________________________________________________640_____` `_____________________________________________________________________________________731_______________________________7` `5kuf(A) : AKQTKIEYGAVEDGSTMTFFKKSKISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMM` `:` `6jfz(A) : AKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSK-pSALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIM` `_____________________________________________________________________________________732_______________________________7` `65________________________________` `5kuf(A) : KEKWWRGNGCPEqNIGGIFIVLAAGLVLSVFVAV` `:` `6jfz(A) : KEKWWRG-----qKIGGIFIVLAAGLVLSVLVAV` `66________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	22.6	1.3	97.3	503 - 504 731 - 732	Bending Region Analysis
1	3	14.4	2.9	87.3	765 - 766	Bending Region Analysis
2	3	22.0	-0.9	86.3	513 - 517 638 - 640	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

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

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

Movement classification: Hinge

PyMOL Script

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