DynDom - Protein Domain Motions

Putative Peptide Abc-Transport System Periplasmic Peptide- Binding Protein

(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	Putative Peptide Abc-Transport System Periplasmic Peptide- Binding Protein
Conformer 1 (PDB)	4oet (A)
Conformer 2 (PDB)	4oev (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	272	0.72	3 - 239 278 - 279 460 - 492
2	218	0.48	240 - 277 280 - 459

Sequence

`________________________________________________________________________________________________________________________` `4oet(A) : KIPKDTLIIAVENEIARINPAYSEDHDAVINLVFSGLTRFDENMSLKPDLAKSWDISKDGLVYDIFLRDDVLWHDGVKFSADDVKFSIEAFKNPKNNSSIYVNFEDIKSVEILNPSHVKI` `:` `4oev(A) : KIPKDTLIIAVENEIARINPAYSEDHDAVINLVFSGLTRFDENMSLKPDLAKSWDISKDGLVYDIFLRDDVLWHDGVKFSADDVKFSIEAFKNPKNNSSIYVNFEDIKSVEILNPSHVKI` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________239_` `4oet(A) : TLFKPYPAFLDALSIGMLPKHLLENENLNTSSFNQNPIGTGPYKFVKWKKGEYVEFKANEHFYLDKVKTPRLIIKHIFDPSIASAELKNGKIDAALIDVSLLNIFKNDENFGILREKSAD` `:` `4oev(A) : TLFKPYPAFLDALSIGMLPKHLLENENLNTSSFNQNPIGTGPYKFVKWKKGEYVEFKANEHFYLDKVKTPRLIIKHIFDPSIASAELKNGKIDAALIDVSLLNIFKNDENFGILREKSAD` `____________________________________________________________________________________________________________________239_` `_________________________________276____________________________________________________________________________________` `4oet(A) : YRALMFNLDNEFLKDLKVRQALNYAVDKESIVKNLLHDYAFVANHPLERSWANSKNFKIYKYDPKKAEDLLVSAGFKKNKDGNFEKDGKILEFEIWAMSNDPLRVSLAGILQSEFRKIGV` `:` `4oev(A) : YRALMFNLDNEFLKDLKVRQALNYAVDKESIVKNLLHDYAFVANHPLERSWANSKNFKIYKYDPKKAEDLLVSAGFKKNKDGNFEKDGKILEFEIWAMSNDPLRVSLAGILQSEFRKIGV` `_________________________________276____________________________________________________________________________________` `________________________________________________________________________________________________459_____________________` `4oet(A) : VSKVVAKPAGSFDYSKVDSFLIGWGSPLDPDFHTFRVFESSQDSALNDEGWNFGHYHDKKVDIALQKARNTSNLEERKKYYKDFIDALYENPPFIFLAYLDFALVYNKDLKGIKTRTLGH` `:` `4oev(A) : VSKVVAKPAGSFDYSKVDSFLIGWGSPLDPDFHTFRVFESSQDSALNDEGWNFGHYHDKKVDIALQKARNTSNLEERKKYYKDFIDALYENPPFIFLAYLDFALVYNKDLKGIKTRTLGH` `________________________________________________________________________________________________459_____________________` `______________` `4oet(A) : HGVGFTWNVYEWSK` `:` `4oev(A) : HGVGFTWNVYEWSK` `______________`

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)	20.7
Translation (A)	0.9
Closure (%)	71.3
Bending Residues ( green )	239 - 240 276 - 281 459 - 460
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