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)	5kf6 (A)
Conformer 2 (PDB)	5kf6 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	614	0.44	16 - 19 140 - 140 154 - 157 162 - 162 166 - 171 385 - 387 538 - 548 561 - 563 570 - 571 576 - 601 603 - 821 836 - 851 860 - 869 873 - 877 887 - 913 920 - 922 926 - 950 958 - 961 966 - 981 989 - 997 1001 - 1216 1219 - 1221
2	582	0.44	20 - 139 141 - 153 158 - 161 163 - 165 172 - 384 388 - 537 549 - 560 564 - 569 572 - 575 602 - 602 822 - 835 852 - 859 870 - 872 878 - 886 914 - 919 923 - 925 951 - 957 962 - 965 982 - 988 998 - 1000 1217 - 1218 1222 - 1229

Sequence

`____19__________________________________________________________________________________________________________139_____` `5kf6(A) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKgVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWrSLFVNA` `:` `5kf6(B) : APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKgVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWrSLFVNA` `____19__________________________________________________________________________________________________________139_____` `______153_____161_165___171_____________________________________________________________________________________________` `5kf6(A) : ATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI` `:` `5kf6(B) : ATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI` `______153_____161_165___171_____________________________________________________________________________________________` `_____________________________________________________________________________________________________________________384` `5kf6(A) : KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD` `:` `5kf6(B) : KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD` `_____________________________________________________________________________________________________________________384` `________________________________________________________________________________________________________________________` `5kf6(A) : GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN` `:` `5kf6(B) : GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYH-------vGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN` `________________________________________________________________________________________________________________________` `______________________________537________548_________560______569_____________________________601_______________________` `5kf6(A) : DPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAADAA` `:` `5kf6(B) : DPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAADAA` `______________________________537________548_________560______569_____________________________601_______________________` `________________________________________________________________________________________________________________________` `5kf6(A) : PDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEGVR` `:` `5kf6(B) : PDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEGVR` `________________________________________________________________________________________________________________________` `__________________________________________________________________________821___________835_____________851_____859_____` `5kf6(A) : ILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTML` `:` `5kf6(B) : ILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTML` `__________________________________________________________________________821___________835_____________851_____859_____` `__869_____877______886___________________908________919___925___________________947_______957_961_965_____________981___` `5kf6(A) : KGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTRLDETIAH` `:` `5kf6(B) : KGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTRLDETIAH` `__869_____877______886___________________908________919___925___________________947_______957_961_965_____________981___` `_988______997___________________________________________________________________________________________________________` `5kf6(A) : VTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILL` `:` `5kf6(B) : VTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILL` `_988______997___________________________________________________________________________________________________________` `____________________________________________________________________________________________________________1216_1221___` `5kf6(A) : VPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTAAAG` `:` `5kf6(B) : VPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTAAAG` `____________________________________________________________________________________________________________1216_1221___` `_______` `5kf6(A) : GNASLMA` `:` `5kf6(B) : GNASLMA` `_______`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	3.4
Translation (A)	0.2
Closure (%)	68.4
Bending Residues ( green )	19 - 20 139 - 141 153 - 159 161 - 163 165 - 166 171 - 172 384 - 385 387 - 388 537 - 538 548 - 549 560 - 561 563 - 564 569 - 576 601 - 603 821 - 822 835 - 836 851 - 852 859 - 860 869 - 874 877 - 878 886 - 887 908 - 914 919 - 920 922 - 923 925 - 941 947 - 951 957 - 958 961 - 962 965 - 966 981 - 982 988 - 989 997 - 998 1000 - 1001 1216 - 1219 1221 - 1222
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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