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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	410	0.7	6 - 170 176 - 197 213 - 216 242 - 345 354 - 374 393 - 473 485 - 497
2	56	1.15	171 - 175 198 - 212 217 - 241 474 - 484
3	26	0.37	346 - 353 375 - 392

Sequence

`________________________________________________________________________________________________________________________` `1uiv(A) : *DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `:` `3mvy(A) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `________________________________________________________________________________________________________________________` `___________________________________________167___________________________197____________212_216______________________241` `1uiv(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `:` `3mvy(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `___________________________________________167___________________________197____________212_216______________________241` `_____________________________________________________________________________________________________345_____353________` `1uiv(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIR` `:` `3mvy(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ` `_____________________________________________________________________________________________________345_____353________` `__________374_______________392______________________________________________________________________________473________` `1uiv(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `:` `3mvy(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `__________374_______________392______________________________________________________________________________473________` `484________________` `1uiv(A) : NIPYAPIATEIPFEQIKPV` `:` `3mvy(A) : NIPYAPIATEIPFEQIKP` `484________________`

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)	8.2
Translation (A)	0.0
Closure (%)	36.5
Bending Residues ( green )	167 - 176 197 - 198 212 - 213 216 - 217 241 - 242 473 - 474 484 - 485
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	6.5
Translation (A)	0.4
Closure (%)	8.4
Bending Residues ( green )	345 - 346 353 - 354 374 - 375 392 - 393
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Shear

PyMOL Script

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