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)	9dl2 (A)
Conformer 2 (PDB)	9dl2 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	636	0.49	17 - 19 125 - 129 132 - 132 140 - 140 154 - 174 539 - 548 562 - 563 567 - 646 648 - 653 656 - 664 669 - 672 674 - 822 837 - 842 844 - 854 864 - 868 873 - 874 887 - 911 920 - 922 925 - 998 1000 - 1087 1090 - 1220
2	568	0.37	16 - 16 20 - 124 130 - 131 133 - 139 141 - 153 175 - 538 549 - 561 564 - 566 647 - 647 654 - 655 665 - 668 673 - 673 823 - 836 843 - 843 855 - 863 869 - 872 875 - 886 912 - 919 923 - 924 999 - 999 1088 - 1089 1221 - 1227

Sequence

`_16_19_________________________________________________________________________________________________121______________` `9dl2(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHsGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSHLs` `:` `9dl2(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGK-sGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSHL-` `_16_19_________________________________________________________________________________________________121______________` `_____________153__________________174___________________________________________________________________________________` `9dl2(A) : RSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIY` `:` `9dl2(B) : rSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIY` `_____________153__________________174___________________________________________________________________________________` `________________________________________________________________________________________________________________________` `9dl2(A) : EGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAE` `:` `9dl2(B) : EGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `9dl2(A) : IKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANS` `:` `9dl2(B) : IKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLE--aNS` `________________________________________________________________________________________________________________________` `______________________________________538_______548__________561__566___________________________________________________` `9dl2(A) : SFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAV` `:` `9dl2(B) : SFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAV` `______________________________________538_______548__________561__566___________________________________________________` `__________________________646____653________664_668_672_________________________________________________________________` `9dl2(A) : RLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPL` `:` `9dl2(B) : RLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPL` `__________________________646____653________664_668_672_________________________________________________________________` `__________________________________________________________________________________822___________836___842_________854___` `9dl2(A) : IAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVA` `:` `9dl2(B) : IAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVA` `__________________________________________________________________________________822___________836___842_________854___` `860_____868_______________886___________________908________919__________________________________________________________` `9dl2(A) : DRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTR` `:` `9dl2(B) : DRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTR` `860_____868_______________886___________________908________919__________________________________________________________` `__________________998_____________________________________________________________________________________1087__________` `9dl2(A) : LDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLH` `:` `9dl2(B) : LDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLH` `__________________998_____________________________________________________________________________________1087__________` `_______________________________________________________________________________________________________________________1` `9dl2(A) : ARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSAS` `:` `9dl2(B) : ARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSAS` `_______________________________________________________________________________________________________________________1` `220_____________` `9dl2(A) : INTAAAGGNASLMAIG` `:` `9dl2(B) : INTAAAGGNASL****` `220_____________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	3.6
Translation (A)	0.1
Closure (%)	80.9
Bending Residues ( green )	16 - 17 19 - 20 121 - 141 153 - 154 174 - 175 538 - 539 548 - 549 561 - 564 566 - 567 646 - 648 653 - 656 664 - 665 668 - 669 672 - 674 822 - 823 836 - 837 842 - 844 854 - 855 860 - 864 868 - 869 871 - 875 886 - 887 908 - 913 919 - 920 922 - 929 998 - 1000 1087 - 1090 1220 - 1221
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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