DynDom - Protein Domain Motions

Oligopeptide-Binding Protein Oppa

(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	Oligopeptide-Binding Protein Oppa
Conformer 1 (PDB)	3drf (A)
Conformer 2 (PDB)	3drj (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	290	0.66	34 - 298 544 - 568
2	245	0.72	299 - 543

Sequence

`________________________________________________________________________________________________________________________` `3drf(A) : ****************GGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGS` `:` `3drj(A) : LKAGNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3drf(A) : DRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSI` `:` `3drj(A) : DRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSI` `________________________________________________________________________________________________________________________` `__________________________________________298___________________________________________________________________________` `3drf(A) : TYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSV` `:` `3drj(A) : TYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSV` `__________________________________________298___________________________________________________________________________` `________________________________________________________________________________________________________________________` `3drf(A) : KGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNF` `:` `3drj(A) : KGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNF` `________________________________________________________________________________________________________________________` `______________________________________________542_______________________________` `3drf(A) : GHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGV*` `:` `3drj(A) : GHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSSA` `______________________________________________542_______________________________`

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)	41.2
Translation (A)	0.1
Closure (%)	99.1
Bending Residues ( green )	298 - 300 542 - 544
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

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