DynDom - Protein Domain Motions

Phosphoglycerate Kinase 1

(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	Phosphoglycerate Kinase 1
Conformer 1 (PDB)	3c3b (A)
Conformer 2 (PDB)	2zgv (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	223	0.58	163 - 176 187 - 408
2	174	0.55	5 - 162 177 - 186 409 - 414

Sequence

`________________________________________________________________________________________________________________________` `3c3b(A) : SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLEN` `:` `2zgv(A) : *LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLEN` `________________________________________________________________________________________________________________________` `_______________________________________162____169_____________185_______________________________________________________` `3c3b(A) : LRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMA` `:` `2zgv(A) : LRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMA` `_______________________________________162____169_____________185_______________________________________________________` `________________________________________________________________________________________________________________________` `3c3b(A) : FTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVK` `:` `2zgv(A) : FTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVK` `________________________________________________________________________________________________________________________` `_________________________________408________` `3c3b(A) : ATSRGCITIIGG-dKVSHVSTGGGASLELLEGKVLPGVDALSNI` `:` `2zgv(A) : ATSRGCITIIGGeDKVSHVSTGGGASLELLEGKVLPGVDALSNI` `_________________________________408________`

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)	-1.0
Closure (%)	99.5
Bending Residues ( green )	162 - 163 169 - 178 185 - 188 408 - 414
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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