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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	630	0.46	93 - 97 139 - 140 154 - 157 166 - 170 375 - 377 483 - 491 539 - 549 560 - 563 568 - 571 577 - 601 604 - 651 656 - 656 659 - 664 672 - 821 837 - 852 861 - 869 873 - 879 884 - 951 958 - 971 974 - 975 977 - 984 989 - 991 994 - 994 1000 - 1007 1010 - 1223 1227 - 1229
2	582	0.45	16 - 92 98 - 138 141 - 153 158 - 165 171 - 374 378 - 482 492 - 538 550 - 559 564 - 567 572 - 576 602 - 603 652 - 655 657 - 658 665 - 671 822 - 836 853 - 860 870 - 872 880 - 883 952 - 957 972 - 973 976 - 976 985 - 988 992 - 993 995 - 999 1008 - 1009 1224 - 1226 1230 - 1230

Sequence

`_____________________________________________________________________________92___97___________________________________1` `7myc(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `:` `7myc(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSH` `_____________________________________________________________________________92___97___________________________________1` `38____________153_157_____165__170______________________________________________________________________________________` `7myc(A) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `:` `7myc(B) : LrSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGI` `38____________153_157_____165__170______________________________________________________________________________________` `___________________________________________________________________________________________________________________374__` `7myc(A) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `:` `7myc(B) : YEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDA` `___________________________________________________________________________________________________________________374__` `_______________________________________________________________________________________________________482______491_____` `7myc(A) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `:` `7myc(B) : EIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGAN` `_______________________________________________________________________________________________________482______491_____` `_______________________________________538________549_______559_563_567_571__576______________________601_______________` `7myc(A) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `:` `7myc(B) : SSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA` `_______________________________________538________549_______559_563_567_571__576______________________601_______________` `________________________________651_655______664____671_________________________________________________________________` `7myc(A) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `:` `7myc(B) : VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETP` `________________________________651_655______664____671_________________________________________________________________` `__________________________________________________________________________________821____________836_____________852____` `7myc(A) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `:` `7myc(B) : LIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDV` `__________________________________________________________________________________821____________836_____________852____` `_860______869_______879_883_________________________________________________________________951___957___________971_____` `7myc(A) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `:` `7myc(B) : ADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHT` `_860______869_______879_883_________________________________________________________________951___957___________971_____` `_____984_988________999____1007_________________________________________________________________________________________` `7myc(A) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `:` `7myc(B) : RLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTL` `_____984_988________999____1007_________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7myc(A) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `:` `7myc(B) : HARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA` `________________________________________________________________________________________________________________________` `___1223_________` `7myc(A) : SINTAAAGGNASLMAI` `:` `7myc(B) : SINTAAAGGNASLMAI` `___1223_________`

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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