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)	1nyq (A)
Conformer 2 (PDB)	1qf6 (A)
Window Length	15
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	399	2.03	231 - 638
2	220	1.82	11 - 230

Sequence

`________________________________________________________________________________________________________________________` `1nyq(A) : INIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFEQIE` `:` `1qf6(A) : PVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALE` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________230__________` `1nyq(A) : KTMKQIVNENMKIERKVVSRDEAKELFSN--DEYKLELIDA-IPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKE` `:` `1qf6(A) : KRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLEEAAK` `___________________________________________________________________________________________________________231__________` `________________________________________________________________________________________________________________________` `1nyq(A) : RDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIAEL` `:` `1qf6(A) : RDHRKIGKQLDLY-HMQEEAPGMVFWHNDGWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSS--ENREYCIKPMNCPGHVQIFNQGLKSYRDLPLRMAEF` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nyq(A) : GTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVKTAM` `:` `1qf6(A) : GSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDMYSTFGFEKIVVKLSTR-PE---KRIGSDEMWDRAEADLAVALEENNIPFEYQLGEGAFYGPKIEFTLYDCL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nyq(A) : GKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNV-DLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPY` `:` `1qf6(A) : DRAWQCGTVQLDFSLPSRLSASYVGEDNERKVPVMIHRAILGSMERFIGILTEEFAGFFPTWLAP--VQVVIMNITDSQSEYVNELTQKLSNAGIRVKADLRNEKIGFKIREHTLRRVPY` `________________________________________________________________________________________________________________________` `__________________________________________________` `1nyq(A) : QIVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR****` `:` `1qf6(A) : MLVCGDKEVESGKVAVRTRRGKDLGSMDVNEVIEKLQQEIRSRSLKQLEE` `__________________________________________________`

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)	16.4
Translation (A)	0.7
Closure (%)	78.0
Bending Residues ( green )	230 - 231
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

PyMOL Script

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