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)	6vz9 (A)
Conformer 2 (PDB)	6vz9 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	615	0.47	122 - 128 156 - 174 539 - 548 560 - 562 568 - 571 577 - 590 592 - 602 605 - 654 657 - 666 669 - 821 836 - 842 844 - 852 859 - 869 886 - 913 919 - 922 925 - 951 957 - 984 996 - 997 1002 - 1007 1009 - 1216 1219 - 1222
2	598	0.53	16 - 121 129 - 155 175 - 538 549 - 559 563 - 567 572 - 576 591 - 591 603 - 604 655 - 656 667 - 668 822 - 835 843 - 843 853 - 858 870 - 885 914 - 918 923 - 924 952 - 956 985 - 995 998 - 1001 1008 - 1008 1217 - 1218 1223 - 1231

Sequence

`_________________________________________________________________________________________________________121____________` `6vz9(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `:` `6vz9(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `_________________________________________________________________________________________________________121____________` `________________155________________174__________________________________________________________________________________` `6vz9(A) : sRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `:` `6vz9(B) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `________________155________________174__________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vz9(A) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `:` `6vz9(B) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vz9(A) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `:` `6vz9(B) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `________________________________________________________________________________________________________________________` `_______________________________________538_______548________559_____567_571________________590_________602______________` `6vz9(A) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `:` `6vz9(B) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `_______________________________________538_______548________559_____567_571________________590_________602______________` `___________________________________654_________666______________________________________________________________________` `6vz9(A) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `:` `6vz9(B) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `___________________________________654_________666______________________________________________________________________` `__________________________________________________________________________________821___________835____842_______852___8` `6vz9(A) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `:` `6vz9(B) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `__________________________________________________________________________________821___________835____842_______852___8` `58________869_____________885____________________908_______918_922__________________________951__956____________________` `6vz9(A) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `:` `6vz9(B) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `58________869_____________885____________________908_______918_922__________________________951__956____________________` `_____984________995__1001__1007_________________________________________________________________________________________` `6vz9(A) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `:` `6vz9(B) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `_____984________995__1001__1007_________________________________________________________________________________________` `____________________________________________________________________________________________________________________1216` `6vz9(A) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `:` `6vz9(B) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `____________________________________________________________________________________________________________________1216` `__1222___________` `6vz9(A) : SINTAAAGGNASLMAIG` `:` `6vz9(B) : SINTAAAGGNASLMAIG` `__1222___________`

Morph

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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 (%)	75.6
Bending Residues ( green )	121 - 129 155 - 156 174 - 175 538 - 539 548 - 549 559 - 560 562 - 563 567 - 568 571 - 577 590 - 592 602 - 605 654 - 657 666 - 669 821 - 822 835 - 836 842 - 844 852 - 853 858 - 859 869 - 870 885 - 886 908 - 914 918 - 919 922 - 929 951 - 952 956 - 957 984 - 985 995 - 998 1001 - 1002 1007 - 1009 1216 - 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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