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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	367	1.0	1004 - 1239 1248 - 1349 1401 - 1429
2	134	1.04	1240 - 1247 1350 - 1400 1430 - 1514

Sequence

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

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	18.1
Translation (A)	0.5
Closure (%)	93.2
Bending Residues ( green )	1239 - 1240 1247 - 1248 1349 - 1350 1400 - 1403 1429 - 1430
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

Download and extract PyMOL PML script file

Download