DynDom - Protein Domain Motions

Pyruvate Kinase

(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	Pyruvate Kinase
Conformer 1 (PDB)	1a49 (B)
Conformer 2 (PDB)	1aqf (H)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	364	0.44	614 - 679 686 - 714 816 - 820 828 - 845 851 - 853 867 - 887 891 - 892 900 - 904 907 - 945 948 - 1031 1033 - 1033 1035 - 1053 1055 - 1055 1058 - 1128
2	151	0.71	680 - 685 715 - 815 821 - 827 846 - 850 854 - 866 888 - 890 893 - 899 905 - 906 946 - 947 1032 - 1032 1034 - 1034 1054 - 1054 1056 - 1057

Sequence

`_________________________________________________________________679___685__________________________714_________________` `1a49(B) : IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEV` `:` `1aqf(H) : IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEV` `__________________________________________________________________79____85__________________________114_________________` `________________________________________________________________________________814___820____827_______________845__850_` `1a49(B) : ELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVH` `:` `1aqf(H) : ELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVH` `________________________________________________________________________________214___220____227_______________245__250_` `____________866__________________887________898___904______________________________________945__________________________` `1a49(B) : EVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL` `:` `1aqf(H) : EVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL` `____________266__________________287________298___304______________________________________345__________________________` `________________________________________________________1031__________________1053______________________________________` `1a49(B) : EAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNL` `:` `1aqf(H) : EAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNL` `_________________________________________________________431___________________453______________________________________` `_______________________________________` `1a49(B) : AMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP` `:` `1aqf(H) : AMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP` `_______________________________________`

Morph

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

Show console

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	4.3
Translation (A)	-0.4
Closure (%)	38.1
Bending Residues ( green )	679 - 680 685 - 686 714 - 715 814 - 816 820 - 821 827 - 828 845 - 846 850 - 851 853 - 854 866 - 867 887 - 888 890 - 893 898 - 900 904 - 907 945 - 948 1031 - 1035 1053 - 1058
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

Download and extract PyMOL PML script file