DynDom - Protein Domain Motions

Glutamate Receptor 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 2
Conformer 1 (PDB)	4u2q (A)
Conformer 2 (PDB)	4u2p (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	249	1.81	397 - 505 637 - 787
2	348	0.85	13 - 380
3	79	2.42	506 - 636
4	21	1.12	788 - 808

Sequence

`________________________________________________________________________________________________________________________` `4u2q(A) : NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQ` `:` `4u2p(A) : IQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u2q(A) : WDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVG--------------------kKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVD` `:` `4u2p(A) : WDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u2q(A) : YDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPR` `:` `4u2p(A) : YDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPR` `________________________________________________________________________________________________________________________` `_________379____________________________________________________________________________________________________________` `4u2q(A) : KIGYWSEVDKMVVTLTED----lEQKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREE` `:` `4u2p(A) : KIGYWSEVDKMVVTLTEDDTSGLEQKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREE` `_________379____________________________________________________________________________________________________________` `_______________505_________________________________________________________________________________636__________________` `4u2q(A) : VIDFSKPFMSLGISIMIKK----spGVFSFLDPLAYEIWMAIVFAYIGVSVVLFLVS-pRSLSARIVAGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGS` `:` `4u2p(A) : VIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMAIVFAYIGVSVVLFLVSRpRSLSARIVAGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGS` `_______________505_________________________________________________________________________________636__________________` `________________________________________________________________________________________________________________________` `4u2q(A) : TKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGEC-` `:` `4u2p(A) : TKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECG` `________________________________________________________________________________________________________________________` `__________787____________________________` `4u2q(A) :` `----------sALSLSNVAGVFYILVGGLGLAMLVALIEFA` `:` `4u2p(A) :` `AKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVAL**` `__________787____________________________`

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)	7.1
Translation (A)	2.7
Closure (%)	88.3
Bending Residues ( green )	379 - 397
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	17.7
Translation (A)	-0.5
Closure (%)	91.7
Bending Residues ( green )	505 - 506 636 - 642
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( violet )	4
Rotation Angle (deg)	17.5
Translation (A)	-1.1
Closure (%)	100.0
Bending Residues ( green )	787 - 790
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

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