DynDom - Protein Domain Motions

Iron-Responsive Element Binding Protein 1

(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	Iron-Responsive Element Binding Protein 1
Conformer 1 (PDB)	2b3x (A)
Conformer 2 (PDB)	2ipy (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	285	1.56	4 - 84 89 - 91 117 - 125 169 - 175 186 - 366 440 - 442 606 - 606
2	328	2.05	85 - 88 92 - 116 147 - 168 183 - 185 607 - 887
3	226	2.82	176 - 182 367 - 435 443 - 605

Sequence

`_________________________________________________________________________________84__88_________________________116_____` `2b3x(A) : SNPFAHLAEPLDPVQPGKKFFNLNKLEDSRYGRLPFSIRVLLEAAIRNCDEFLVKKQDIENILHWNVTQHKNIEVPFKPARVILQDFTGVPAVVDFAAMRDAVKKLGGDPEKINPVCPAD` `:` `2ipy(A) : SNPFAYLAEPLDPAQPGKKFFNLNKLDYSRYGRLPFSIRVLLEAAVRNCDKFLVKKEDIENILNWNVTQHMNIEVPFKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDPEKINPICPVD` `_________________________________________________________________________________84__88_________________________116_____` `_125________________________________________168_172_176______185________________________________________________________` `2b3x(A) : LVIDHSIQVDFNRRADSLQKNQDLEFERNRERFEFLKWGSQAFHNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGILGWGVGGIEAEAVMLGQPISMVLPQ` `:` `2ipy(A) : LVID---------------------fERNRERFEFLKWGSKAFRNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGVLGWGVGGIEAEAVMLGQPISMVLPQ` `_125________________________________________168_172_176______185________________________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : VIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATAAFFPVDEVSITYLVQTGRDEEKLKYIKKYLQAVGMFRDFNDPSQDPDFTQVVEL` `:` `2ipy(A) : VIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATATFFPVDEVSIKYLVQTGRDESKVKQIRKYLQAVGMFRDYSDPSQDPDFTQVVEL` `________________________________________________________________________________________________________________________` `__366__________________________________________________________________435______________________________________________` `2b3x(A) : DLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPEHHNDHKTFIYDNTEFTLAHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVDAGLNVMPYIKTSLSPGSGVVTYY` `:` `2ipy(A) : DLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPDHHNDHKTFIYNDSEFTLSHGSVVIAAITSSTNTSNPSVMLGAGLLAKKAVDAGLNVKPYVKTSLSPGSGVVTYY` `__366__________________________________________________________________435______________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : LQESGVMPYLSQLGFDVVGYGCMTCIGNSGPLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGVNAKGQQVFLKDIWPTRDEIQAVER` `:` `2ipy(A) : LRESGVMPYLSQLGFDV-------------pLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGTNAKGQQVFLRDIWPTREEIQAVER` `________________________________________________________________________________________________________________________` `__606___________________________________________________________________________________________________________________` `2b3x(A) : QYVIPGMFKEVYQKIETVNESWNALATPSDKLFFWNSKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAVMAR` `:` `2ipy(A) : QYVIPGMFTEVYQKIETVNAS-------sDKLYLWNPKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAIMAR` `__606___________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : GTFANIRLLNRFLNKQAPQTIHLPSGEILDVFDAAERYQQAGLPLIVLAGKEYGAGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADALGLTGQERYTIIIPE` `:` `2ipy(A) : GTFANIRLLNRFLNKQAPQTIHLPSGETLDVFDAAERYQQEGHPLIVLAGKEYGSGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADSLGLTGRERYTIIIPE` `________________________________________________________________________________________________________________________` `________________________________________________` `2b3x(A) : NLKPQMKVQVKLDTGKTFQAVMRFDTDVELTYFLNGGILNYMIRKMAK` `:` `2ipy(A) : NLTPRMHVQVKLDTGKTFQAVIRFDTDVELTYFHNGGILNYMIRKMAK` `________________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	27.1	-1.7	69.4	84 - 85 88 - 92 116 - 117 125 - 148 168 - 169 185 - 186 606 - 631	Bending Region Analysis
1	3	41.2	2.0	97.4	172 - 182 366 - 367 435 - 443 605 - 606	Bending Region Analysis
2	3	62.6	-6.4	99.2	176 - 183 605 - 631	Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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