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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	640	0.39	18 - 18 20 - 159 170 - 538 549 - 560 564 - 566 572 - 576 594 - 594 602 - 603 647 - 647 652 - 655 657 - 658 667 - 669 815 - 818 822 - 835 852 - 857 870 - 886 914 - 921 923 - 925 951 - 957 964 - 966 984 - 988 990 - 993 997 - 1000 1007 - 1009 1084 - 1090 1217 - 1231
2	573	0.42	16 - 17 19 - 19 160 - 169 539 - 548 561 - 563 567 - 571 577 - 593 595 - 601 604 - 646 648 - 651 656 - 656 659 - 666 670 - 814 819 - 821 836 - 851 858 - 869 887 - 913 922 - 922 926 - 950 958 - 963 967 - 983 989 - 989 994 - 996 1001 - 1006 1010 - 1083 1091 - 1216

Sequence

`__17____________________________________________________________________________________________________________________` `7mya(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `:` `7mya(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `__17____________________________________________________________________________________________________________________` `____________________159_______169_______________________________________________________________________________________` `7mya(A) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `:` `7mya(B) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `____________________159_______169_______________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7mya(A) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `:` `7mya(B) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7mya(A) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `:` `7mya(B) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `________________________________________________________________________________________________________________________` `_______________________________________538_______548_________560___566__571___________________593_____601_______________` `7mya(A) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `:` `7mya(B) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `_______________________________________538_______548_________560___566__571___________________593_____601_______________` `___________________________646__651_655________666______________________________________________________________________` `7mya(A) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `:` `7mya(B) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `___________________________646__651_655________666______________________________________________________________________` `___________________________________________________________________________814_818______________835_____________851_____` `7mya(A) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `:` `7mya(B) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `___________________________________________________________________________814_818______________835_____________851_____` `__________869______________886______895_______________________921_925___________________947_______957___963_____________` `7mya(A) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `:` `7mya(B) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `__________869______________886______895_______________________921_925___________________947_______957___963_____________` `____983__988__993___1000__1006_________________________________________________________________________1083___1090______` `7mya(A) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `:` `7mya(B) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `____983__988__993___1000__1006_________________________________________________________________________1083___1090______` `____________________________________________________________________________________________________________________1216` `7mya(A) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `:` `7mya(B) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `____________________________________________________________________________________________________________________1216` `_________________` `7mya(A) : SINTAAAGGNASLMAIG` `:` `7mya(B) : SINTAAAGGNASLMAIG` `_________________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	3.0
Translation (A)	0.1
Closure (%)	73.8
Bending Residues ( green )	17 - 20 159 - 160 169 - 170 538 - 539 548 - 549 560 - 561 563 - 564 566 - 567 571 - 577 593 - 595 601 - 604 646 - 648 651 - 652 655 - 659 666 - 667 669 - 670 814 - 815 818 - 819 821 - 822 835 - 836 851 - 852 854 - 858 869 - 870 886 - 887 895 - 914 921 - 923 925 - 931 947 - 951 957 - 958 963 - 964 966 - 968 983 - 984 988 - 990 993 - 994 996 - 997 1000 - 1001 1006 - 1007 1009 - 1010 1083 - 1084 1090 - 1091 1216 - 1217
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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