DynDom - Protein Domain Motions

Oligo-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	Oligo-Peptide Binding Protein
Conformer 1 (PDB)	1rkm
Conformer 2 (PDB)	2rkm (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	291	0.52	3 - 248 254 - 269 487 - 515
2	222	0.67	249 - 253 270 - 486

Sequence

`________________________________________________________________________________________________________________________` `1rkm : ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIAN` `:` `2rkm(A) : ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIAN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rkm : IDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE` `:` `2rkm(A) : IDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE` `________________________________________________________________________________________________________________________` `____247___________________269___________________________________________________________________________________________` `1rkm : IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLT` `:` `2rkm(A) : IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLT` `____247___________________269___________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rkm : FDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV` `:` `2rkm(A) : FDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV` `________________________________________________________________________________________________________________________` `__485________________________________` `1rkm : PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH` `:` `2rkm(A) : PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH` `__485________________________________`

Morph

Morph animation in progress.
Status: Initialising

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)	25.9
Translation (A)	0.0
Closure (%)	95.6
Bending Residues ( green )	247 - 254 269 - 271 485 - 488
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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