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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	451	0.87	6 - 198 213 - 216 235 - 473 478 - 478 484 - 497
2	41	0.92	199 - 212 217 - 234 474 - 477 479 - 483

Sequence

`________________________________________________________________________________________________________________________` `1uiv(A) : *DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `:` `3mvw(A) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `________________________________________________________________________________________________________________________` `__________________________________________________________________________198___________212_216_______________234_______` `1uiv(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `:` `3mvw(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `__________________________________________________________________________198___________212_216_______________234_______` `________________________________________________________________________________________________________________________` `1uiv(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIR` `:` `3mvw(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________________473_477___4` `1uiv(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `:` `3mvw(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `_____________________________________________________________________________________________________________473_477___4` `83_________________` `1uiv(A) : NIPYAPIATEIPFEQIKPV` `:` `3mvw(A) : NIPYAPIATEIPFEQIKP` `83_________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	8.5
Translation (A)	-0.1
Closure (%)	35.7
Bending Residues ( green )	198 - 199 212 - 213 216 - 217 234 - 235 473 - 474 477 - 479 483 - 484
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

Download and extract PyMOL PML script file

Download