DynDom - Protein Domain Motions

Atp-Dependent Phosphoenolpyruvate Carboxykinase

(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	Atp-Dependent Phosphoenolpyruvate Carboxykinase
Conformer 1 (PDB)	1j3b (B)
Conformer 2 (PDB)	2pc9 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	361	0.52	4 - 229 237 - 239 244 - 342 365 - 370 391 - 421 516 - 517 525 - 526
2	145	1.17	230 - 236 240 - 243 343 - 364 371 - 390 422 - 515 518 - 524

Sequence

`________________________________________________________________________________________________________________________` `1j3b(B) : QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTE` `:` `2pc9(B) : QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTE` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________________229____236____2` `1j3b(B) : SPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTL` `:` `2pc9(B) : SPWHALFARNMFILPRRF--------fVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTL` `_________________________________________________________________________________________________________229____236____2` `43________________________________________________________________________________________________342___________________` `1j3b(B) : STDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSP` `:` `2pc9(B) : STDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSP` `43________________________________________________________________________________________________342___________________` `364_______________390___________________________420_____________________________________________________________________` `1j3b(B) : EEAMYYFLSGYTARV-pRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETW` `:` `2pc9(B) : EEAMYYFLSGYTARtEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETW` `364_______________390___________________________420_____________________________________________________________________` `_______________________515______524____` `1j3b(B) : ADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT` `:` `2pc9(B) : ADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT` `_______________________515______524____`

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)	12.5
Translation (A)	0.2
Closure (%)	93.4
Bending Residues ( green )	229 - 230 236 - 240 243 - 248 342 - 343 364 - 371 390 - 396 420 - 422 515 - 518 524 - 525
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

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