DynDom - Protein Domain Motions

Periplasmic Murein 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	Periplasmic Murein Peptide-Binding Protein
Conformer 1 (PDB)	3o9p (A)
Conformer 2 (PDB)	4toz (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	195	0.79	267 - 361 371 - 389 404 - 484
2	287	0.61	9 - 266 485 - 513
3	23	0.85	362 - 370 390 - 403

Sequence

`________________________________________________________________________________________________________________________` `3o9p(A) : ******TVLAEKQELVRHIKDEPASLDPAKAVGLPEIQVIRDLFEGLVNQNEKGEIVPGVATQWKSNDNRIWTFTLRDNAKWADGTPVTAQDFVYSWQRLVDPKTLSPFAWFAALAGINN` `:` `4toz(A) : AEVPSGTVLAEKQELVRHIKDEPASLDPAKAVGLPEIQVIRDLFEGLVNQNEKGEIVPGVATQWKSNDNRIWTFTLRDNAKWADGTPVTAQDFVYSWQRLVDPKTLSPFAWFAALAGINN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3o9p(A) : AQAIIDGKATPDQLGVTAVDAHTLKIQLDKPLPWFVNLTANFAFFPVQKANVESGKEWTKPGNLIGNGAYVLKERVVNEKLVVVPNTHYWDNAKTVLQKVTFLPINQESAATKRYLAGDI` `:` `4toz(A) : AQAIIDGKATPDQLGVTAVDAHTLKIQLDKPLPWFVNLTANFAFFPVQKANVESGKEWTKPGNLIGNGAYVLKERVVNEKLVVVPNTHYWDNAKTVLQKVTFLPINQESAATKRYLAGDI` `________________________________________________________________________________________________________________________` `_____________________264___________________________________________________________________________________________358__` `3o9p(A) : DITESFPKNMYQKLLKDIPGQVYTPPQLGTYYYAFNTQKGPTADQRVRLALSMTIDRRLMTEKVLGTGEKPAWHFTPDVTAGFTPEPSPFEQMSQEELNAQAKTLLSAAGYGPQKPLKLT` `:` `4toz(A) : DITESFPKNMYQKLLKDIPGQVYTPPQLGTYYYAFNTQKGPTADQRVRLALSMTIDRRLMTEKVLGTGEKPAWHFTPDVTAGFTPEPSPFEQMSQEDLNAQAKTLLSAAGYGPQKPLKLT` `_____________________286___________________________________________________________________________________________380__` `_______370_______380_________________400________________________________________________________________________________` `3o9p(A) : LLYNTSENHQKIAIAVASMWKKNLGVDVKLQNQEWKTYIDSRNTGNFDVIRASWVGDYNEPSTFLTLLTSTHSGNISRFNNPAYDKVLAQASTENTVKARNADYNAAEKILMEQAPIAPI` `:` `4toz(A) : LLYNTSENHQKIAIAVASMWKKNLGVDVKLQNQEWKTYIDSRNTGNFDVIRASWVGDYNEPSTFLTLLTSTHSGNISRFNNPAYDKVLAQASTENTVKARNADYNAAEKILMEQAPIAPI` `_______392_______402_________________422________________________________________________________________________________` `483________________________________` `3o9p(A) : YQYTNGRLIKPWLKGYPINNPEDVAYSRTMYIVKH` `:` `4toz(A) : YQYTNGRLIKPWLKGYPINNPEDVAYSRTMYIVKH` `505________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	50.4
Translation (A)	0.4
Closure (%)	87.3
Bending Residues ( green )	264 - 269 483 - 487
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	17.7
Translation (A)	0.0
Closure (%)	94.0
Bending Residues ( green )	358 - 362 370 - 371 380 - 390 400 - 404
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

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