DynDom - Protein Domain Motions

Glycyl-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	Glycyl-Trna Synthetase
Conformer 1 (PDB)	2pmf (A)
Conformer 2 (PDB)	2zt7 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	467	2.12	67 - 164 194 - 196 216 - 671
2	48	0.7	165 - 193 197 - 215

Sequence

`___________________________________________________________________________________________________164__________________` `2pmf(A) : DIVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKK` `:` `2zt7(A) : IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKK` `___________________________________________________________________________________________________164__________________` `_______192_196________________215_______________________________________________________________________________________` `2pmf(A) : SEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVD` `:` `2zt7(A) : SEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVD` `_______192_196________________215_______________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2pmf(A) : PSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMEN-----aCDCWDAESKTSYGWIEIVGCADRSCYDLSCHARrF` `:` `2zt7(A) : PSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARAT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2pmf(A) : QKTL-----YVEEVVPNVIEPSFRLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT` `:` `2zt7(A) : KVPLVAEKPyVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT` `________________________________________________________________________________________________________________________` `____________________________________________________` `2pmf(A) : VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEG` `:` `2zt7(A) : VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFE` `____________________________________________________`

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)	14.9
Translation (A)	-0.9
Closure (%)	66.7
Bending Residues ( green )	164 - 165 192 - 194 196 - 197 215 - 216
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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