5' Polynucleotide Kinase-3' Phosphatase Catalytic Domain

(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 5' Polynucleotide Kinase-3' Phosphatase Catalytic Domain
  Conformer 1
(PDB)
1yj5 (B)
  Conformer 2
(PDB)
1yj5 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 191 0.5   146 - 338
2 179 0.58   339 - 520

Sequence


           ________________________________________________________________________________________________________________________ 
 1yj5(B) : RKSSLGWESLKKLLVFTASGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKLVIFTNQgIGRGKLPAEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKP 
         :                                                                                                                          
 1yj5(A) : ****LGWESLKKLLVFTASGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKLVIFTNQgIGRGKLPAEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________336_____________________________________________ 
 1yj5(B) : VSGwDHLQEQANEGIPISVEDSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFI 
         :                                                                                                                          
 1yj5(A) : VSGwDHLQEQANEGIPISVEDSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFI 
           ________________________________________________________________________336_____________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1yj5(B) : QEHLVSAGYVHVNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREtDPSHAPVSDvfSYRKQFEPPTLAEGFLEILEIPFRL 
         :                                                                                                                          
 1yj5(A) : QEHLVSAGYVHVNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREtDPSHAPVSDvfSYRKQFEPPTLAEGFLEILEIPFRL 
           ________________________________________________________________________________________________________________________ 

           __________________                                                                                                       
 1yj5(B) : QEHLDPALQRLYRQFSEG                                                                                                       
         :                                                                                                                          
 1yj5(A) : QEHLDPALQRLYRQFSEG                                                                                                       
           __________________                                                                                                       

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)
10.6
Translation
(A)
0.3
Closure
(%)
25.5
Bending Residues
( green )
  336 - 339
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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