DynDom - Protein Domain Motions

Threonyl-Trna Synthetase

(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
Conformer 1 (PDB)	1qf6 (A)
Conformer 2 (PDB)	1nyq (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	405	1.76	232 - 636
2	225	1.93	4 - 231

Sequence

`________________________________________________________________________________________________________________________` `1qf6(A) : *PVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVE` `:` `1nyq(B) : MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFE` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________________231_______` `1qf6(A) : ALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLEE` `:` `1nyq(B) : QIEKTMKQIVNENMKIERKVVSRDEAKELFSN--DEYKLELIDA-IPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEE` `______________________________________________________________________________________________________________230_______` `________________________________________________________________________________________________________________________` `1qf6(A) : AAKRDHRKIGKQLDLY-HMQEEAPGMVFWHNDGWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSS--ENREYCIKPMNCPGHVQIFNQGLKSYRDLPLRM` `:` `1nyq(B) : RKERDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1qf6(A) : AEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDMYSTFGFEKIVVKLSTR-PE---KRIGSDEMWDRAEADLAVALEENNIPFEYQLGEGAFYGPKIEFTLY` `:` `1nyq(B) : AELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1qf6(A) : DCLDRAWQCGTVQLDFSLPSRLSASYVGEDNERKVPVMIHRAILGSMERFIGILTEEFAGFFPTWLAPVQVVIMNIT-DSQSEYVNELTQKLSNAGIRVKADLRNEKIGFKIREHTLRRV` `:` `1nyq(B) : TAMGKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKI` `________________________________________________________________________________________________________________________` `____________________________________________________` `1qf6(A) : PYMLVCGDKEVESGKVAVRTRRGKDLGSMDVNEVIEKLQQEIRSRSLKQLEE` `:` `1nyq(B) : PYQIVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR**` `____________________________________________________`

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)	20.7
Translation (A)	0.5
Closure (%)	32.5
Bending Residues ( green )	231 - 232
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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