DynDom - Protein Domain Motions

Phosphoenolpyruvate Carboxykinase, Cytosolic [Gtp]

(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	Phosphoenolpyruvate Carboxykinase, Cytosolic [Gtp]
Conformer 1 (PDB)	3dt7 (A)
Conformer 2 (PDB)	3dt7 (B)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	306	0.4	7 - 83 89 - 94 115 - 248 277 - 278 329 - 341 346 - 419
2	299	0.52	84 - 88 95 - 114 249 - 276 279 - 328 342 - 345 420 - 619

Sequence

`___________________________________________________________________________________83___88____94_________________114____` `3dt7(A) : GSMPPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMS` `:` `3dt7(B) : *****QLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMS` `___________________________________________________________________________________83___88____94_________________114____` `________________________________________________________________________________________________________________________` `3dt7(A) : EEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGN` `:` `3dt7(B) : EEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGN` `________________________________________________________________________________________________________________________` `_______248____________________271______________________________________________________328_____336______________________` `3dt7(A) : SLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFT` `:` `3dt7(B) : SLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFT` `_______248____________________271______________________________________________________328_____336______________________` `__________________________________________________________419___________________________________________________________` `3dt7(A) : NVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHD` `:` `3dt7(B) : NVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEA--------kVIMHD` `__________________________________________________________419___________________________________________________________` `________________________________________________________________________________________________________________________` `3dt7(A) : PFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLED` `:` `3dt7(B) : PFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLED` `________________________________________________________________________________________________________________________` `________________________` `3dt7(A) : QVNADLPYEIERELRALKQRISQM` `:` `3dt7(B) : QVNADLPYEIERELRALKQRISQM` `________________________`

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)	3.9
Translation (A)	0.1
Closure (%)	97.8
Bending Residues ( green )	83 - 84 88 - 89 94 - 95 114 - 122 248 - 249 271 - 279 328 - 329 336 - 348 419 - 420
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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