DynDom - Protein Domain Motions

Threonyl-Trna Synthetase 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	Threonyl-Trna Synthetase 1
Conformer 1 (PDB)	1nyr (B)
Conformer 2 (PDB)	1nyr (A)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	402	1.16	240 - 641
2	219	1.48	13 - 239

Sequence

`________________________________________________________________________________________________________________________` `1nyr(B) : MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFE` `:` `1nyr(A) : ***INIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFE` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________239_` `1nyr(B) : QIEKTMKQIVNENMKIERKVVSRDEAKEL--------eLIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKE` `:` `1nyr(A) : QIEKTMKQIVNENMKIERKVVSRDEAKELFSNDEYKLELIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKE` `____________________________________________________________________________________________________________________239_` `________________________________________________________________________________________________________________________` `1nyr(B) : RDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIAEL` `:` `1nyr(A) : RDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIAEL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nyr(B) : GTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVKTAM` `:` `1nyr(A) : GTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVKTAM` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nyr(B) : GKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQ` `:` `1nyr(A) : GKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQ` `________________________________________________________________________________________________________________________` `_____________________________________________` `1nyr(B) : IVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR` `:` `1nyr(A) : IVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR` `_____________________________________________`

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)	10.1
Translation (A)	-1.3
Closure (%)	9.8
Bending Residues ( green )	239 - 240
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

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