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)	3dri (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	292	0.52	34 - 298 477 - 478 544 - 568
2	243	0.73	299 - 476 479 - 543

Sequence

`________________________________________________________________________________________________________________________` `3drf(A) : ****************GGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGS` `:` `3dri(A) : LKAGNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3drf(A) : DRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSI` `:` `3dri(A) : DRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSI` `________________________________________________________________________________________________________________________` `_________________________________________297____________________________________________________________________________` `3drf(A) : TYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSV` `:` `3dri(A) : TYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSV` `_________________________________________297____________________________________________________________________________` `___________________________________________________________________________________________________475__________________` `3drf(A) : KGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNF` `:` `3dri(A) : KGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNF` `___________________________________________________________________________________________________475__________________` `_______________________________________________543_____________________________` `3drf(A) : GHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGV` `:` `3dri(A) : GHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSS` `_______________________________________________543_____________________________`

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)	37.9
Translation (A)	0.3
Closure (%)	96.8
Bending Residues ( green )	297 - 300 475 - 479 543 - 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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