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)	7myb (A)
Conformer 2 (PDB)	7myb (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	639	0.44	16 - 124 130 - 131 133 - 155 158 - 161 175 - 539 549 - 558 564 - 567 572 - 577 593 - 594 601 - 603 647 - 647 656 - 657 666 - 668 673 - 674 822 - 835 843 - 844 852 - 862 869 - 886 914 - 916 923 - 924 940 - 941 951 - 962 964 - 969 974 - 975 985 - 995 998 - 1000 1006 - 1009 1015 - 1015 1083 - 1085 1087 - 1087 1217 - 1218 1222 - 1230
2	573	0.49	125 - 129 132 - 132 156 - 157 162 - 174 540 - 548 559 - 563 568 - 571 578 - 592 595 - 600 604 - 646 648 - 655 658 - 665 669 - 672 675 - 821 836 - 842 845 - 851 863 - 868 887 - 913 917 - 922 925 - 939 942 - 950 963 - 963 970 - 973 976 - 984 996 - 997 1001 - 1005 1010 - 1014 1016 - 1082 1086 - 1086 1088 - 1216 1219 - 1221

Sequence

`____________________________________________________________________________________________________________124_________` `7myb(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `:` `7myb(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `____________________________________________________________________________________________________________124_________` `________________155___161__________174__________________________________________________________________________________` `7myb(A) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `:` `7myb(B) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `________________155___161__________174__________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7myb(A) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `:` `7myb(B) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7myb(A) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `:` `7myb(B) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `________________________________________________________________________________________________________________________` `________________________________________539______548_______558__563_567_571___577____________592_____600________________` `7myb(A) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `:` `7myb(B) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `________________________________________539______548_______558__563_567_571___577____________592_____600________________` `___________________________646______655_______665____672________________________________________________________________` `7myb(A) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `:` `7myb(B) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `___________________________646______655_______665____672________________________________________________________________` `__________________________________________________________________________________821___________835____842______851_____` `7myb(A) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `:` `7myb(B) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `__________________________________________________________________________________821___________835____842______851_____` `___862___868_______________886___________________908_____916___922______________939_____947____________962____969_973___` `7myb(A) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `:` `7myb(B) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `___862___868_______________886___________________908_____916___922______________939_____947____________962____969_973___` `_____984________995_1000_1005_____1014________________________________________________________________1082______________` `7myb(A) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `:` `7myb(B) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `_____984________995_1000_1005_____1014________________________________________________________________1082______________` `____________________________________________________________________________________________________________________1216` `7myb(A) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `:` `7myb(B) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `____________________________________________________________________________________________________________________1216` `_1221____________` `7myb(A) : SINTAAAGGNASLMAIG` `:` `7myb(B) : SINTAAAGGNASLMAI*` `_1221____________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	2.9
Translation (A)	0.2
Closure (%)	72.8
Bending Residues ( green )	92 - 93 97 - 98 138 - 141 153 - 154 157 - 158 165 - 166 170 - 171 374 - 375 377 - 378 482 - 489 491 - 495 538 - 539 549 - 550 559 - 560 563 - 564 567 - 568 571 - 572 576 - 577 601 - 604 651 - 652 655 - 659 664 - 665 671 - 672 821 - 822 836 - 837 852 - 853 860 - 862 869 - 870 872 - 873 879 - 880 883 - 884 951 - 952 957 - 958 971 - 977 984 - 985 988 - 989 991 - 995 999 - 1000 1007 - 1010 1223 - 1224 1226 - 1230
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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