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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	284	0.52	34 - 298 478 - 478 544 - 568
2	238	0.84	299 - 477 479 - 543

Sequence

`________________________________________________________________________________________________________________________` `3drf(A) : ************GGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWT` `:` `3fto(A) : NFDVAYQNPDKAIKGGNLKVAYQSDSP-kAQWLSGLSNDATFAT-sGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3drf(A) : DSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEV` `:` `3fto(A) : DSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKE-kPG-tQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEV` `________________________________________________________________________________________________________________________` `______________________________________298_______________________________________________________________________________` `3drf(A) : VSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYE` `:` `3fto(A) : VSTAKSVAALSSSKYDIING-vSSQYKQVKNLKGYKVLGQQA-yISL-yYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYE` `______________________________________298_______________________________________________________________________________` `______________________________________________________________________________________________474_______________________` `3drf(A) : KQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFN` `:` `3fto(A) : KQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKL-eFNSWVDH-tTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFN` `______________________________________________________________________________________________474_______________________` `__________________________________________543__________________________________` `3drf(A) : DSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGV****` `:` `3fto(A) : DSEITKDLNDIDSAKSENPTYRKAAFVKYQED-nKKAYVIPTNF-lNYTPVNKRVVG-tLDYGA-nTWSEIGVSSAKLA` `__________________________________________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)	37.7
Translation (A)	0.3
Closure (%)	97.3
Bending Residues ( green )	298 - 301 474 - 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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