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)	3mz9 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	443	0.79	6 - 198 213 - 216 242 - 473 484 - 497
2	49	0.86	199 - 212 217 - 241 474 - 483

Sequence

`________________________________________________________________________________________________________________________` `1uiv(A) : **DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `:` `3mz9(A) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `________________________________________________________________________________________________________________________` `__________________________________________________________________________198___________212_216______________________241` `1uiv(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `:` `3mz9(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `__________________________________________________________________________198___________212_216______________________241` `________________________________________________________________________________________________________________________` `1uiv(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIR` `:` `3mz9(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________________473_______4` `1uiv(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `:` `3mz9(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `_____________________________________________________________________________________________________________473_______4` `83_________________` `1uiv(A) : NIPYAPIATEIPFEQIKPV` `:` `3mz9(A) : NIPYAPIATEIPFEQIKPV` `83_________________`

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)	7.7
Translation (A)	-0.1
Closure (%)	36.6
Bending Residues ( green )	198 - 199 212 - 213 216 - 217 241 - 242 473 - 474 483 - 484
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Mixed

PyMOL Script

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