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)
2noo (A)
  Conformer 2
(PDB)
1uiu (A)
  Window Length 9
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 243 1.41   8 - 226   240 - 247   398 - 399   470 - 477   487 - 492
2 243 0.95   227 - 239   248 - 397   400 - 469   478 - 486   493 - 495

Sequence


           ________________________________________________________________________________________________________________________ 
 2noo(A) : DEITTAWPVNVGPLNPHLATPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQAHAALELANQIVDVKALSKTELQITLK 
         :                                                                                                                          
 1uiu(A) : DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLK 
           ________________________________________________________________________________________________________________________ 

           ____________________________________________________________________________________________________226_________________ 
 2noo(A) : SAYYPFLQELALPAPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLS 
         :                                                                                                                          
 1uiu(A) : SAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLS 
           ____________________________________________________________________________________________________226_________________ 

           _247____________________________________________________________________________________________________________________ 
 2noo(A) : QPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVP-aNLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQAD 
         :                                                                                                                          
 1uiu(A) : QPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIRAD 
           _247____________________________________________________________________________________________________________________ 

           _______________________________397_____________________________________________________________________469___475_______4 
 2noo(A) : MRQIGADVSLIGEEESSI-aRQRDGRFGMIFHRTAGAPADPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNI 
         :                                                                                                                          
 1uiu(A) : MRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNI 
           _______________________________397_____________________________________________________________________469___475_______4 

           85____492_______                                                                                                         
 2noo(A) : PYAPIATEIPFEQIKP                                                                                                         
         :                                                                                                                          
 1uiu(A) : PYAPIATEIPFEQIKP                                                                                                         
           85____492_______                                                                                                         

Morph

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


Show console


play backwards pause play forwards

Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
7.8
Translation
(A)
0.4
Closure
(%)
16.8
Bending Residues
( green )
  226 - 240
  247 - 248
  397 - 403
  469 - 470
  475 - 481
  485 - 487
  492 - 495
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