DynDom - Protein Domain Motions

Glutamate Dehydrogenase, Nad-Specific Glutamate Dehydrogenase, Glutamate Dehydrogenase

(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 Dehydrogenase, Nad-Specific Glutamate Dehydrogenase, Glutamate Dehydrogenase
Conformer 1 (PDB)	2yfh (A)
Conformer 2 (PDB)	2yfh (F)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	270	0.38	4 - 214 247 - 249 372 - 403 406 - 414 432 - 446
2	169	0.98	215 - 246 250 - 371 404 - 405 415 - 431

Sequence

`________________________________________________________________________________________________________________________` `2yfh(A) : MSKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTL` `:` `2yfh(F) : *SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTL` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________213___________________________` `2yfh(A) : PMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSG` `:` `2yfh(F) : PMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSG` `__________________________________________________________________________________________213___________________________` `___246__________________________________________________________________________________________________________________` `2yfh(A) : NVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEI----DGRVADYAKEFGLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQ` `:` `2yfh(F) : NVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQ` `___246__________________________________________________________________________________________________________________` `________371_____________________________403______412________________431_________________` `2yfh(A) : AGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW` `:` `2yfh(F) : AGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW` `________371_____________________________403______412________________431_________________`

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)	7.2
Translation (A)	0.1
Closure (%)	14.2
Bending Residues ( green )	213 - 215 246 - 250 371 - 372 403 - 410 412 - 418 431 - 432
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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