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) 		2vpn (A)
  Conformer 2
(PDB) 		3gyy (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 135 0.97   4 - 62   68 - 72   85 - 122   210 - 246
2 41 0.86   63 - 63   67 - 67   73 - 79   81 - 84   207 - 209   282 - 306
3 120 1.0   64 - 66   80 - 80   123 - 206   250 - 281

Sequence


           ________________________________________________________62___67__________79___84__________________________________121___ 
 2vpn(A) : DNWRYAHEEYEGDVQDVFAQAFKGYVEDNSDHTVQVYRFGELdIMEQTQNGILQFVNQSPGFTGSLIPSAQIFFIPYLMPTDMDTVLEFFDESKAINEMFPKLYAEHGLELLKMYPEGEM 
         :                                                                                                                          
 3gyy(A) : DNWRYAHEEYEGDVQDVFAQAFKGYVEDNSDHTVQVYRFGELGiMEQTQNGILQFVNQSPGFTGSLIPSAQIFFIPYLMPTDMDTVLEFFDESKAINEMFPKLYAEHGLELLKMYPEGEM 
           ________________________________________________________62___67__________79___84__________________________________121___ 

           __________________________________________________________________________________209__________________________________2 
 2vpn(A) : VVTADEPITSPEDFDNKKIRTMTNPLLAETYKAFGATPTPLPWGEVYGGLQTGIIDGQENPIFWIESGGLYEVSPNLTFTSHGWFTTAMMANQDFYEGLSEEDQQLVQDAADAAYDHTIE 
         :                                                                                                                          
 3gyy(A) : VVTADEPITSPEDFDnKKIRTMTNPLLAETYKAFGATPTPLPWGEVYGGLQTGIIDGQENPIFWIESGGLYEVSPNLTFTSHGWFTTAMMANQDFYEGLSEEDQQLVQDAADAAYDHTIE 
           __________________________________________________________________________________209__________________________________2 

           46________________________________281_____________________________                                                       
 2vpn(A) : HIKGLSEESLEKIKAASDEVTVTRLNDEQIQAFKERAPQVEEKFIEMTGEQGQELLDQFKADLKAV                                                       
         :                                                                                                                          
 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 12.8 0.4 9.5   62 - 63   67 - 75   84 - 88   209 - 210 Bending Region Analysis
1 3 22.4 1.4 95.5   62 - 64   66 - 72   121 - 124   246 - 254 Bending Region Analysis
3 2 16.0 0.2 49.7   63 - 64   66 - 67   79 - 81   206 - 208   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 3 ———› Residue 2

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

Movement classification: Hinge

PyMOL Script

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