DynDom - Protein Domain Motions

Glutamate--Trna Ligase

(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	Glutamate--Trna Ligase
Conformer 1 (PDB)	8vc5 (A)
Conformer 2 (PDB)	9y81 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	402	1.85	5 - 379 382 - 383 407 - 419 444 - 447 449 - 467 472 - 478
2	67	1.64	380 - 381 384 - 406 420 - 443 448 - 448 468 - 471 479 - 491

Sequence

`________________________________________________________________________________________________________________________` `8vc5(A) : MTTVRTRIAPSPTGDPHVGTAYIALFNLCFARQHGGQFILRIEDTDQLRSTRESEQQIYDALRWLGIEWDEGPDVGGPHGPYRQSERGHIYKKYSDELVEKGHAFTCFCTPERLDAVRAE` `:` `9y81(B) : NVRVRVAPSPTGDPHVGTAYMALFNEIFAKRFKGKMILRIEDTDRTRSRQDYEENIFSALRWCGIQWDEGPDVGGPYGPYRQSERTKIYQGYVETLLKTDCAYKCFATPQELAEMRA-` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8vc5(A) :` `QMARKETPRYDGHCMHLPKDEVQRRLAAGESHVTRMKVPTEGVCVVPDMLRGDVEIPWDRMDMQVLMKADGLPTYFLANVVDDHLMGITHVLRGEEWLPSAPKLIKLYEYFGWEQPQLCY` `:` `9y81(B) :` `--------rYR----YLSPEEVASREAAGQPYTIRLKVPLSGECVFEDYSKGRVVFPWADVDDQVLVKSDGFPTYHFANVIDDHLMGITHVLRGEEWLSSTPKHLLLYEAFGWEPPVFLH` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8vc5(A) : MPLLRNPDKSKLSKRKNPTSITFYERMGYLPQALLNYLGRMGWS-----eKFTLAEMIEHFDLSRVSLGGPIFDLEKLSWLNGQWI-REQSVEEFAREVQKWALNPEYLMKIAPHVQGRV` `:` `9y81(B) : MPLLLNPDGTKLSKRKNPTSIFYYRDSGYVKEAFVNFLTLMGYSMEGDEEVYSLERIIETFNPRRIGKSGAVFDIQKLDWMNKHYLNHEGSPECLLKELQGWLLNDEFFLKILPLCQSRI` `________________________________________________________________________________________________________________________` `_______________377__________________________406__________419______________________443_447_________________467_471____478` `8vc5(A) : ENFSQIAPLAGFFFSGGVPLDASLFEHKKLDPTQVRQVLQLVLWKLESLRQWEKERITGCIQAVAEHLQLKLRD-VMPLMFPAITGHASSVSVLDAMEILGADLSRYRLRQALELLGGAS` `:` `9y81(B) : TTLAEFINLTSFFFSGLLEYRVEELLPQALSPEKAAILLYSYVKYLEKTDQWTKETCYLGSKWLAQAFNVHHKKAIIPLLYVAITGKKQGLPLFDSIEILGKPRARARLVYAEKLLGGVP` `_______________393__________________________422__________435______________________460_464_________________484_488____495` `_______________________` `8vc5(A) : KKETKEWEKIRDAIP******` `:` `9y81(B) : KKLAATVDKFMQREDFEEATFDL` `_______________________`

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)	18.4
Translation (A)	-0.6
Closure (%)	95.5
Bending Residues ( green )	377 - 388 406 - 407 419 - 420 443 - 444 447 - 449 467 - 468 471 - 472 478 - 479
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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