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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	447	0.86	6 - 198 213 - 214 216 - 216 235 - 473 486 - 497
2	45	0.94	199 - 212 215 - 215 217 - 234 474 - 485

Sequence

`________________________________________________________________________________________________________________________` `1uiv(A) : *DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `:` `3mvz(A) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT` `________________________________________________________________________________________________________________________` `__________________________________________________________________________198___________212___________________234_______` `1uiv(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `:` `3mvz(A) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ` `__________________________________________________________________________198___________212___________________234_______` `________________________________________________________________________________________________________________________` `1uiv(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIR` `:` `3mvz(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________________473________` `1uiv(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `:` `3mvz(A) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG` `_____________________________________________________________________________________________________________473________` `_485_______________` `1uiv(A) : NIPYAPIATEIPFEQIKPV` `:` `3mvz(A) : NIPYAPIATEIPFEQIKP` `_485_______________`

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)	8.7
Translation (A)	-0.2
Closure (%)	36.7
Bending Residues ( green )	198 - 199 212 - 217 234 - 235 473 - 474 485 - 486
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