DynDom - Protein Domain Motions

Phosphoenolpyruvate Carboxykinase [Atp]

(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 [Atp]
Conformer 1 (PDB)	1yvy (A)
Conformer 2 (PDB)	1ytm (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	367	1.0	4 - 239 248 - 349 401 - 429
2	134	1.04	240 - 247 350 - 400 430 - 514

Sequence

`________________________________________________________________________________________________________________________` `1yvy(A) : SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGAN` `:` `1ytm(B) : SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGAN` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________________239__` `1yvy(A) : ENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFF` `:` `1ytm(B) : ENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFF` `__________________________________________________________________________________________________________________1239__` `___247___________________________________________________________________________________________________349____________` `1yvy(A) : GLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGV` `:` `1ytm(B) : GLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGV` `__1247__________________________________________________________________________________________________1349____________` `____________________________________400__________________________429____________________________________________________` `1yvy(A) : LPPVSILSKEQTKYYFLSGFTAK----------pTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELK` `:` `1ytm(B) : LPPVSILSKEQTKYYFLSGFTAKLAGTERGITEPTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELK` `___________________________________1400_________________________1429____________________________________________________` `_____________________________________` `1yvy(A) : GVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF` `:` `1ytm(B) : GVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF` `_____________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	18.1
Translation (A)	0.5
Closure (%)	94.8
Bending Residues ( green )	239 - 240 247 - 248 349 - 350 400 - 403 429 - 430
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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