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)	1uiu (A)
Conformer 2 (PDB)	1uiv (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	265	0.99	6 - 126 128 - 219 224 - 247 470 - 497
2	227	0.85	127 - 127 220 - 223 248 - 469

Sequence

`________________________________________________________________________________________________________________________` `1uiu(A) : DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLK` `:` `1uiv(A) : DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLK` `________________________________________________________________________________________________________________________` `126__________________________________________________________________________________________219________________________` `1uiu(A) : SAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLS` `:` `1uiv(A) : SAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLS` `126__________________________________________________________________________________________219________________________` `_247____________________________________________________________________________________________________________________` `1uiu(A) : QPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIRAD` `:` `1uiv(A) : QPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIRAD` `_247____________________________________________________________________________________________________________________` `_______________________________________________________________________________________________________469______________` `1uiu(A) : MRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNI` `:` `1uiv(A) : MRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNI` `_______________________________________________________________________________________________________469______________` `_________________` `1uiu(A) : PYAPIATEIPFEQIKP*` `:` `1uiv(A) : PYAPIATEIPFEQIKPV` `_________________`

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)	16.9
Translation (A)	0.1
Closure (%)	79.4
Bending Residues ( green )	126 - 128 219 - 224 247 - 249 469 - 470
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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