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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	454	16.42	5 - 403 415 - 421 433 - 438 465 - 473 486 - 487 497 - 500 505 - 510 647 - 652 678 - 683 703 - 718 729 - 738 744 - 746 762 - 769
2	87	0.93	404 - 414 428 - 432 439 - 464 474 - 485 488 - 496 501 - 504 739 - 743 747 - 761
3	161	10.7	511 - 646 653 - 677 684 - 702 719 - 728 770 - 807

Sequence

`________________________________________________________________________________________________________________________` `6jfz(B) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `:` `6jfy(A) : HVIRIGGIFEYADGPNAQVMNAEEHAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQGSTTNAVQSICNALEVPHIQLRWKHHPLDNKDTFYVNLY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6jfz(B) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `:` `6jfy(A) : PDYASLSHAILDLVQSLKWRSATVVYDDSTGLIRLQELIMAPSRYNIRLKIRQLPIDSDDSRPLLKEMKRGREFRIIFDCSHTMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDLEPYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6jfz(B) : YSGVNLTGFRILNVDNPHVSAIVEKWSMER-dGVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEK` `:` `6jfy(A) : YSGVNLTGFRILNVDNPHVSAIVEKWSMERLQgVMMTDAALLYDAVHIVSVTYQRAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEK` `________________________________________________________________________________________________________________________` `________384____________414_______________432_____________________________464__________________485________496_____504____` `6jfz(B) : VGVWSPADGLNItNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLG` `:` `6jfy(A) : VGVWSPADGLNI-nRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLG` `________384____________414_______________432_____________________________464__________________485________496_____504____` `_________________________________________________________________________________________646____________________________` `6jfz(B) : VSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIARaLSTRIIGGIWWFFTLIIISSYTANLAAFLTVE----pIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFE` `:` `6jfy(A) : VSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSVVLFVIAR-lSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFE` `_________________________________________________________________________________________646____________________________` `677___683________________702_______________________728___734______743_______________761_________________________________` `6jfz(B) : KMWAFMSSKpSALVKNNeEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRG-qKIGGIFIVLAAGLVLSVLVAV` `:` `6jfy(A) : KMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSqKIGGIFIVLAAGLVLSVLVAV` `677___683________________702_______________________728___734______743_______________761_________________________________`

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)	168.7
Translation (A)	18.5
Closure (%)	34.4
Bending Residues ( green )	384 - 404 414 - 428 432 - 439 464 - 474 485 - 488 496 - 502 504 - 510 734 - 739 743 - 747 761 - 769
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	151.7
Translation (A)	-13.1
Closure (%)	11.1
Bending Residues ( green )	505 - 511 646 - 653 677 - 681 683 - 691 702 - 719 728 - 732 762 - 771
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

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