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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	290	1.77	4 - 84 89 - 91 117 - 127 169 - 175 186 - 366 440 - 442 606 - 606 623 - 633
2	325	2.07	85 - 88 92 - 116 146 - 168 183 - 185 607 - 622 634 - 887
3	227	2.82	176 - 182 367 - 435 443 - 605

Sequence

`_________________________________________________________________________________84__88_________________________116_____` `2b3x(A) : SNPFAHLAEPLDPVQPGKKFFNLNKLEDSRYGRLPFSIRVLLEAAIRNCDEFLVKKQDIENILHWNVTQHKNIEVPFKPARVILQDFTGVPAVVDFAAMRDAVKKLGGDPEKINPVCPAD` `:` `3snp(A) : SNPFAYLAEPLDPAQPGKKFFNLNKLDYSRYGRLPFSIRVLLEAAVRNCDKFLVKKEDIENILNWNVTQHMNIEVPFKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDPEKINPICPVD` `_________________________________________________________________________________84__88_________________________116_____` `124_________________________________________168_172_176______185________________________________________________________` `2b3x(A) : LVIDHSIQVDFNRRADSLQKNQDLEFERNRERFEFLKWGSQAFHNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGILGWGVGGIEAEAVMLGQPISMVLPQ` `:` `3snp(A) : LVIDHS------------------eFERNRERFEFLKWGSKAFRNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGVLGWGVGGIEAEAVMLGQPISMVLPQ` `124_________________________________________168_172_176______185________________________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : VIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATAAFFPVDEVSITYLVQTGRDEEKLKYIKKYLQAVGMFRDFNDPSQDPDFTQVVEL` `:` `3snp(A) : VIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATATFFPVDEVSIKYLVQTGRDESKVKQIRKYLQAVGMFRDYSDPSQDPDFTQVVEL` `________________________________________________________________________________________________________________________` `__366__________________________________________________________________435______________________________________________` `2b3x(A) : DLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPEHHNDHKTFIYDNTEFTLAHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVDAGLNVMPYIKTSLSPGSGVVTYY` `:` `3snp(A) : DLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPDHHNDHKTFIYNDSEFTLSHGSVVIAAITSSTNTSNPSVMLGAGLLAKKAVDAGLNVKPYVKTSLSPGSGVVTYY` `__366__________________________________________________________________435______________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : LQESGVMPYLSQLGFDVVGYGCMTCIGNSGPLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGVNAKGQQVFLKDIWPTRDEIQAVER` `:` `3snp(A) : LRESGVMPYLSQLGFDVV------------pLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGTNAKGQQVFLRDIWPTREEIQAVER` `________________________________________________________________________________________________________________________` `__606________________________633________________________________________________________________________________________` `2b3x(A) : QYVIPGMFKEVYQKIETVNESWNALATPSDKLFFWNSKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAVMAR` `:` `3snp(A) : QYVIPGMFTEVYQKIETVNASW--------kLYLWNPKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAIMAR` `__606________________________633________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2b3x(A) : GTFANIRLLNRFLNKQAPQTIHLPSGEILDVFDAAERYQQAGLPLIVLAGKEYGAGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADALGLTGQERYTIIIPE` `:` `3snp(A) : GTFANIRLLNRFLNKQAPQTIHLPSGETLDVFDAAERYQQEGHPLIVLAGKEYGSGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADSLGLTGRERYTIIIPE` `________________________________________________________________________________________________________________________` `________________________________________________` `2b3x(A) : NLKPQMKVQVKLDTGKTFQAVMRFDTDVELTYFLNGGILNYMIRKMAK` `:` `3snp(A) : NLTPRMHVQVKLDTGKTFQAVIRFDTDVELTYFHNGGILNYMIRKMAK` `________________________________________________`

Morph

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	26.7	-1.5	67.1	84 - 85 88 - 92 116 - 117 124 - 149 168 - 169 185 - 186 606 - 623 633 - 634	Bending Region Analysis
1	3	41.3	2.1	96.5	172 - 182 366 - 367 435 - 443 605 - 606	Bending Region Analysis
2	3	62.7	-6.4	99.0	176 - 183 605 - 622	Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 2 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 2

Movement classification: Hinge

PyMOL Script

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