DynDom - Protein Domain Motions

Monomeric Diphtheria Toxin 3

(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	Monomeric Diphtheria Toxin 3
Conformer 1 (PDB)	1mdt (A)
Conformer 2 (PDB)	1ddt
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	373	1.28	3 - 387
2	146	1.16	388 - 533

Sequence

`________________________________________________________________________________________________________________________` `1mdt(A) : GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT` `:` `1ddt : GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1mdt(A) : EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAsCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQ` `:` `1ddt : EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAsCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1mdt(A) : TALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVH` `:` `1ddt : TALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVH` `________________________________________________________________________________________________________________________` `___378__________________________________________________________________________________________________________________` `1mdt(A) : NSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFH` `:` `1ddt : NSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFH` `___378__________________________________________________________________________________________________________________` `___________________________________________` `1mdt(A) : RSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS` `:` `1ddt : RSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS` `___________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	176.0
Translation (A)	0.4
Closure (%)	95.2
Bending Residues ( green )	378 - 388
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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