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)	1yae (A)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	54	14.55	125 - 172 189 - 194
2	31	9.95	94 - 124
3	28	9.39	173 - 187 195 - 207

Sequence

`________________________________________________________________________________________________________________________` `5kuf(A) : THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPD` `:` `1yae(A) : **************************************************************************************PANITDSLSNRSLIVTTILEEPYVLFKKSDKP` `________________________________________________________________________________________________________________________` `124_____________________________________________172____________187____194_______________________________________________` `5kuf(A) : FSSLSRAILDLVQFFKWKTVTVVYDDSTGLIRLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHEMAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYS` `:` `1yae(A) : LYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRK----------------------------` `455_____________________________________________503____________518____525_______________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) :` `GVNMTGFRILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRTDFDLDVI` `:` `1yae(A) :` `-------------------------------------------------iDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLME` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : SLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADL` `:` `1yae(A) : STTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC**************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : AVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQT` `:` `1yae(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5kuf(A) : KIEYGAVEDGSTMTFFKKSKISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKW` `:` `1yae(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `______________________________` `5kuf(A) : WRGNGCPEqNIGGIFIVLAAGLVLSVFVAV` `:` `1yae(A) : ****************************` `______________________________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	154.2
Translation (A)	0.9
Closure (%)	89.4
Bending Residues ( green )	124 - 125
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	139.3
Translation (A)	12.7
Closure (%)	42.1
Bending Residues ( green )	172 - 173 187 - 189 194 - 195
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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