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)	5kuh (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	139	0.61	7 - 107 214 - 251
2	106	0.56	108 - 213

Sequence

`________________________________________________________________________________________________________________________` `2f36(A) : **********************************************************************************************************************` `:` `5kuh(A) : THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `5kuh(A) : FSSLSRAILDLVQFFKWKTVTVVYDDSTGLIRLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHEMAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : ********************************************************************************************************************` `:` `5kuh(A) : GVNMTGFRILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRTDFDLDVI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2f36(A) : **********************TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQND-KGEWNGMVKELIDHRADLAVAPLTITYVREK` `:` `5kuh(A) : SLKEEGLEKIGTWDPASGLNMTEsNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLTITYVREK` `________________________________________________________________________________________________________________________` `_____105_______________________________________________________________________________________________________211______` `2f36(A) : VIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYG` `:` `5kuh(A) : VIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVEDGSTMTFFKKSKISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQRNCNLTQIGGLIDSKGYG` `_____502_______________________________________________________________________________________________________728______` `_________________________________________` `2f36(A) : VGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPS` `:` `5kuh(A) : VGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRG***` `_________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	27.8
Translation (A)	0.6
Closure (%)	99.4
Bending Residues ( green )	105 - 110 211 - 214
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

Download and extract PyMOL PML script file

Download