DynDom - Protein Domain Motions

Nickel-Binding Periplasmic 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	Nickel-Binding Periplasmic Protein
Conformer 1 (PDB)	1uiv (A)
Conformer 2 (PDB)	3e3k (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	269	1.0	6 - 242 442 - 442 445 - 447 471 - 498
2	224	0.68	243 - 441 443 - 444 448 - 470

Sequence

`________________________________________________________________________________________________________________________` `1uiv(A) : **DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `:` `3e3k(A) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________________________24` `1uiv(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `:` `3e3k(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `______________________________________________________________________________________________________________________24` `2_______________________________________________________________________________________________________________________` `1uiv(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIR` `:` `3e3k(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ` `2_______________________________________________________________________________________________________________________` `_____________________________________________________________________________441___447____________________470___________` `1uiv(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `:` `3e3k(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `_____________________________________________________________________________441___447____________________470___________` `___________________` `1uiv(A) : NIPYAPIATEIPFEQIKPV` `:` `3e3k(A) : NIPYAPIATEIPFEQIKPV` `___________________`

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)	10.6
Translation (A)	0.0
Closure (%)	85.6
Bending Residues ( green )	242 - 243 441 - 445 447 - 448 470 - 471
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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