Periplasmic Substrate Binding 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 Periplasmic Substrate Binding Protein
  Conformer 1
(PDB) 		2vpo (A)
  Conformer 2
(PDB) 		3gyy (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 138 0.96   4 - 62   68 - 73   85 - 122   208 - 246
2 123 1.07   63 - 66   80 - 80   123 - 207   249 - 281
3 35 0.72   74 - 79   81 - 84   282 - 306

Sequence


           ________________________________________________________62__66___________79__83___________________________________121___ 
 2vpo(A) : DNWRYAHEEYEGDVQDVFAQAFKGYVEDNSDHTVQVYRFGELdIMEQTQNGILQFVNQSPGFTGSLIPSAQIFFIPYLMPTDMDTVLEFFDESKAINEMFPKLYAEHGLELLKMYPEGEM 
         :                                                                                                                          
 3gyy(A) : DNWRYAHEEYEGDVQDVFAQAFKGYVEDNSDHTVQVYRFGELGiMEQTQNGILQFVNQSPGFTGSLIPSAQIFFIPYLMPTDMDTVLEFFDESKAINEMFPKLYAEHGLELLKMYPEGEM 
           ________________________________________________________62__66___________79__83___________________________________121___ 

           ________________________________________________________________________________207____________________________________2 
 2vpo(A) : VVTADEPITSPEDFDNKKIRTMTNPLLAETYKAFGATPTPLPWGEVYGGLQTGIIDGQENPIFWIESGGLYEVSPNLTFTSHGWFTTAMMANQDFYEGLSEEDQQLVQDAADAAYDHTIE 
         :                                                                                                                          
 3gyy(A) : VVTADEPITSPEDFDnKKIRTMTNPLLAETYKAFGATPTPLPWGEVYGGLQTGIIDGQENPIFWIESGGLYEVSPNLTFTSHGWFTTAMMANQDFYEGLSEEDQQLVQDAADAAYDHTIE 
           ________________________________________________________________________________207____________________________________2 

           46________________________________281______________________________                                                      
 2vpo(A) : HIKGLSEESLEKIKAASDEVTVTRLNDEQIQAFKERAPQVEEKFIEMTGEQGQELLDQFKADLKAVQ                                                      
         :                                                                                                                          
 3gyy(A) : HIKGLSEESLEKIKAASDEVTVTRLNDEQIQAFKERAPQVEEKFIEMTGEQGQELLDQFKADLK***                                                      
           46________________________________281______________________________                                                      

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 21.7 1.3 95.0   62 - 63   66 - 73   121 - 123   207 - 209   246 - 254 Bending Region Analysis
1 3 13.6 0.3 8.4   68 - 75   83 - 87 Bending Region Analysis
2 3 15.6 0.0 41.9   79 - 81   281 - 282 Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 2 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 2

Movement classification: Hinge

PyMOL Script

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