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)
1zlq (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 264 1.62   6 - 126   128 - 243   471 - 497
2 226 0.68   127 - 127   244 - 470

Sequence


           ________________________________________________________________________________________________________________________ 
 2noo(A) : **DEITTAWPVNVGPLNPHLATPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQAHAALELANQIVDVKALSKTELQIT 
         :                                                                                                                          
 1zlq(B) : APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQIT 
           ________________________________________________________________________________________________________________________ 

           _125___________________________________________________________________________________________________________________2 
 2noo(A) : LKSAYYPFLQELALPAPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ 
         :                                                                                                                          
 1zlq(B) : LKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQ 
           _125___________________________________________________________________________________________________________________2 

           43______________________________________________________________________________________________________________________ 
 2noo(A) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVP-aNLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ 
         :                                                                                                                          
 1zlq(B) : LSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQ 
           43______________________________________________________________________________________________________________________ 

           __________________________________________________________________________________________________________470___________ 
 2noo(A) : ADMRQIGADVSLIGEEESSI-aRQRDGRFGMIFHRTAGAPADPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG 
         :                                                                                                                          
 1zlq(B) : ADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELG 
           __________________________________________________________________________________________________________470___________ 

           ___________________                                                                                                      
 2noo(A) : NIPYAPIATEIPFEQIKP*                                                                                                      
         :                                                                                                                          
 1zlq(B) : NIPYAPIATEIPFEQIKPV                                                                                                      
           ___________________                                                                                                      

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
27.3
Translation
(A)
1.9
Closure
(%)
80.2
Bending Residues
( green )
  125 - 128
  243 - 248
  470 - 471
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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