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

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

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

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

PyMOL Script

Download and extract PyMOL PML script file

Download