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 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	367	0.44	614 - 704 709 - 712 810 - 811 814 - 817 824 - 827 830 - 835 839 - 854 867 - 882 890 - 1030 1035 - 1053 1055 - 1055 1059 - 1072 1077 - 1125
2	145	0.63	705 - 708 713 - 809 812 - 813 818 - 823 828 - 829 836 - 838 855 - 866 883 - 889 1031 - 1034 1054 - 1054 1056 - 1058 1073 - 1076

Sequence

`__________________________________________________________________________________________704_708_712___________________` `1a49(B) : IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEV` `:` `1aqf(B) : IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEV` `__________________________________________________________________________________________104_108_112___________________` `___________________________________________________________________________809___________823_827_____835________________` `1a49(B) : ELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVH` `:` `1aqf(B) : ELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVH` `___________________________________________________________________________209___________223_227_____235________________` `854_________866_____________882____889__________________________________________________________________________________` `1a49(B) : EVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL` `:` `1aqf(B) : EVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL` `254_________266_____________282____289__________________________________________________________________________________` `_______________________________________________________1030___________________1053_1058__________1072___________________` `1a49(B) : EAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNL` `:` `1aqf(B) : EAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNL` `________________________________________________________430_434________________453__458___________472___________________` `_______________________________________` `1a49(B) : AMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP` `:` `1aqf(B) : AMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP` `_______________________________________`

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)	3.5
Translation (A)	-0.3
Closure (%)	27.9
Bending Residues ( green )	704 - 705 708 - 709 712 - 713 809 - 818 823 - 824 827 - 830 835 - 836 838 - 839 854 - 855 866 - 867 882 - 883 889 - 890 1030 - 1031 1034 - 1035 1053 - 1056 1058 - 1059 1072 - 1073 1075 - 1085
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