DynDom - Protein Domain Motions

Bifunctional Protein Puta

(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	Bifunctional Protein Puta
Conformer 1 (PDB)	6x9d (A)
Conformer 2 (PDB)	6x9d (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	619	0.36	16 - 17 20 - 121 130 - 156 158 - 158 173 - 538 549 - 559 564 - 567 572 - 576 591 - 591 601 - 603 642 - 643 647 - 647 654 - 657 659 - 659 667 - 670 673 - 675 822 - 836 853 - 859 870 - 886 914 - 919 923 - 925 951 - 956 972 - 974 985 - 988 990 - 992 997 - 999 1006 - 1008 1083 - 1085 1089 - 1090 1218 - 1218 1223 - 1231
2	594	0.48	18 - 19 122 - 129 157 - 157 159 - 172 539 - 548 560 - 563 568 - 571 577 - 590 592 - 600 604 - 641 644 - 646 648 - 653 658 - 658 660 - 666 671 - 672 676 - 821 837 - 852 860 - 869 887 - 913 920 - 922 926 - 950 957 - 971 975 - 984 989 - 989 993 - 996 1000 - 1005 1009 - 1082 1086 - 1088 1091 - 1217 1219 - 1222

Sequence

`__17____________________________________________________________________________________________________120_____________` `6x9d(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `:` `6x9d(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `__17____________________________________________________________________________________________________120_____________` `__________________156_____________172___________________________________________________________________________________` `6x9d(A) : LsRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRG` `:` `6x9d(B) : L-rSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRG` `__________________156_____________172___________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6x9d(A) : IYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWD` `:` `6x9d(B) : IYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6x9d(A) : AEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGA` `:` `6x9d(B) : AEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGA` `________________________________________________________________________________________________________________________` `________________________________________538_______548________559_563_567_571________________590_______600_______________` `6x9d(A) : NSSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARR` `:` `6x9d(B) : NSSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARR` `________________________________________538_______548________559_563_567_571________________590_______600_______________` `_______________________641__646____653_657______666_670__675____________________________________________________________` `6x9d(A) : AVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEET` `:` `6x9d(B) : AVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEET` `_______________________641__646____653_657______666_670__675____________________________________________________________` `___________________________________________________________________________________821____________836_____________852__8` `6x9d(A) : PLIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQED` `:` `6x9d(B) : PLIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQED` `___________________________________________________________________________________821____________836_____________852__8` `57_________869______________886___________________908________919___925___________________947______956____________971____` `6x9d(A) : VADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLH` `:` `6x9d(B) : VADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLH` `57_________869______________886___________________908________919___925___________________947______956____________971____` `______984_988_992_996_____1005_________________________________________________________________________1082__1088_______` `6x9d(A) : TRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYT` `:` `6x9d(B) : TRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYT` `______984_988_992_996_____1005_________________________________________________________________________1082__1088_______` `______________________________________________________________________________________________________________________12` `6x9d(A) : LHARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVS` `:` `6x9d(B) : LHARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVS` `______________________________________________________________________________________________________________________12` `17_1222___________` `6x9d(A) : ASINTAAAGGNASLMAIG` `:` `6x9d(B) : ASINTAAAGGNASLMAIG` `17_1222___________`

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)	3.2
Translation (A)	0.0
Closure (%)	80.1
Bending Residues ( green )	17 - 20 120 - 140 156 - 159 172 - 173 538 - 539 548 - 549 559 - 560 563 - 564 567 - 568 571 - 577 590 - 592 600 - 601 603 - 604 641 - 644 646 - 648 653 - 654 657 - 660 666 - 667 670 - 673 675 - 676 821 - 822 836 - 837 852 - 853 857 - 865 869 - 874 886 - 887 908 - 914 919 - 920 922 - 923 925 - 927 947 - 951 956 - 957 971 - 972 974 - 975 984 - 985 988 - 990 992 - 993 996 - 997 999 - 1000 1005 - 1006 1008 - 1009 1082 - 1083 1085 - 1086 1088 - 1091 1217 - 1219 1222 - 1223
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Shear

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