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)	9dl4 (A)
Conformer 2 (PDB)	9dl4 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	683	0.46	17 - 18 92 - 102 122 - 123 125 - 128 140 - 141 143 - 145 159 - 176 384 - 389 478 - 479 483 - 484 539 - 548 559 - 646 649 - 665 669 - 809 816 - 820 826 - 827 836 - 841 845 - 855 857 - 859 867 - 870 873 - 881 884 - 998 1000 - 1219
2	506	0.41	19 - 91 103 - 121 124 - 124 129 - 139 142 - 142 146 - 153 177 - 383 390 - 477 480 - 482 485 - 538 549 - 558 647 - 648 666 - 668 810 - 815 821 - 825 828 - 835 842 - 844 856 - 856 860 - 866 871 - 872 882 - 883 999 - 999

Sequence

`_17____________________________________________________________________91________102________________121___________138___` `9dl4(A) : PAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKgVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSHLsRSL` `:` `9dl4(B) : PAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKgVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGNWKSHL-rSL` `_17____________________________________________________________________91________102________________121___________138___` `__145_____153____________________176____________________________________________________________________________________` `9dl4(A) : FVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGP` `:` `9dl4(B) : FVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGP` `__145_____153____________________176____________________________________________________________________________________` `________________________________________________________________________________________________________________________` `9dl4(A) : GISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKR` `:` `9dl4(B) : GISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKR` `________________________________________________________________________________________________________________________` `383___389_____________________________________________________________________________________477__482__________________` `9dl4(A) : AQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLgANSSFVHR` `:` `9dl4(B) : AQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLgANSSFVHR` `383___389_____________________________________________________________________________________477__482__________________` `_________________________________538_______548_______558________________________________________________________________` `9dl4(A) : INDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAAD` `:` `9dl4(B) : INDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAAD` `_________________________________538_______548_______558________________________________________________________________` `_____________________646________________665_____________________________________________________________________________` `9dl4(A) : AAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEG` `:` `9dl4(B) : AAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEG` `_____________________646________________665_____________________________________________________________________________` `________________________________________________________________809___815__820__825_______835___841___________855_859___` `9dl4(A) : VRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILT` `:` `9dl4(B) : VRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILT` `________________________________________________________________809___815__820__825_______835___841___________855_859___` `_866_870________881_____________________________________________________________________________________________________` `9dl4(A) : MLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTRLDETI` `:` `9dl4(B) : MLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLTFGLHTRLDETI` `_866_870________881_____________________________________________________________________________________________________` `_____________998________________________________________________________________________________________________________` `9dl4(A) : AHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRI` `:` `9dl4(B) : AHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRI` `_____________998________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `9dl4(A) : LLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTAA` `:` `9dl4(B) : LLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTAA` `________________________________________________________________________________________________________________________` `_____` `9dl4(A) : AGGNA` `:` `9dl4(B) : *****` `_____`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	3.1
Translation (A)	0.1
Closure (%)	74.2
Bending Residues ( green )	17 - 19 91 - 92 102 - 103 121 - 132 138 - 143 145 - 146 153 - 159 176 - 177 383 - 384 389 - 390 477 - 480 482 - 487 538 - 539 548 - 549 558 - 559 646 - 649 665 - 666 668 - 669 809 - 810 815 - 816 820 - 821 825 - 828 835 - 836 841 - 842 844 - 845 855 - 857 859 - 860 866 - 867 870 - 873 881 - 884 998 - 1000
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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