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)	2pme (A)
Conformer 2 (PDB)	2zt5 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	422	1.19	67 - 143 227 - 243 246 - 279 283 - 289 294 - 671
2	92	0.78	144 - 226 244 - 245 280 - 282 290 - 293

Sequence

`______________________________________________________________________________143_______________________________________` `2pme(A) : DIVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKK` `:` `2zt5(A) : IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKK` `______________________________________________________________________________143_______________________________________` `_________________________________________226______________243_________________________________279_______289_293_________` `2pme(A) : SEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVD` `:` `2zt5(A) : SEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVD` `_________________________________________226______________243_________________________________279_______289_293_________` `________________________________________________________________________________________________________________________` `2pme(A) : PSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMEN-----aCDCWDAESKTSYGWIEIVGCADRSCYDLSCHARkR` `:` `2zt5(A) : PSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARAT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2pme(A) :` `----FQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREG--qRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT` `:` `2zt5(A) :` `KVPLVAEKPyVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT` `________________________________________________________________________________________________________________________` `____________________________________________________` `2pme(A) : VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEG` `:` `2zt5(A) : VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFE` `____________________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	13.8
Translation (A)	-1.0
Closure (%)	76.6
Bending Residues ( green )	143 - 144 226 - 227 243 - 246 279 - 283 289 - 290 293 - 294
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

Download and extract PyMOL PML script file

Download