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)	6vu9 (A)
Conformer 2 (PDB)	1nyr (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	390	2.56	242 - 631
2	226	1.88	5 - 241

Sequence

`________________________________________________________________________________________________________________________` `6vu9(A) : **NITLPDGSRREFENPVSVMEVAQSIGAGLAKATIAGAVDGVLVDASDVIDHDASLRIITAKDEEGVEIIRHSCAHLVGHAVKQLYPDVKMVIGPVIAEGFYYDIYSERPFTPDDMA` `:` `1nyr(B) : MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vu9(A) : AIEKRMGELIAQDYDVIKKMTPRAEVIEIFKARGEDYKLRLIEDMSEDIQAMGMYYHQEYVDMCRGPHVPNTRFLKAFKLTRISGAYWRGDAQNEQLQRIYGTAWADKKQLEAYIKRIEE` `:` `1nyr(B) : QIEKTMKQIVNENMKIERKVVSRDEAKE----------LeLIDAIPED-ENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEE` `________________________________________________________________________________________________________________________` `241_____________________________________________________________________________________________________________________` `6vu9(A) : AEMRDHRRIGKQQDLF-HLQEEAPGLVFWHPKGWALWQVVEQYMRKVYRNSGYGEVRCPQILDVSLWKKSGHWDNYQDNMF--FTESEKRTYAVKPMNCPGHIQVFNQGLHSYRDLPIRY` `:` `1nyr(B) : RKERDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRI` `240_____________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vu9(A) : GEFGSCHRNEPSGALHGILRVRGFTQDDGHVFCTENQIESEVTAFHQQALAVYQHFGFDEIQIKIALR-PESR---LGDDATWDKAEGALRSALTACGVEWQELPGEGAFYGPKIEYHLK` `:` `1nyr(B) : AELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vu9(A) : DAIGRTWQLGTMQVDFMMPGRLGAEYVDENSQKKHPVMLHRAIVGSMERFLGILIEHHAGQFPAWLAPTQVVVANIT-DAQADYVSGVTKTLAEQGFRVSSDLRNEKIGYKIREHTLQRV` `:` `1nyr(B) : TAMGKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKI` `________________________________________________________________________________________________________________________` `________________________________________________` `6vu9(A) : PYLLVIGDREKENGAVAVRTRSGEDLGSMSLQAFIERLHAEGA***` `:` `1nyr(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)	50.8
Translation (A)	0.1
Closure (%)	99.0
Bending Residues ( green )	241 - 242
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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