Difference between revisions of "Structural Alignments (Phenylketonuria)"

From Bioinformatikpedia
(Dataset generation)
(Explore structural alignments)
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=== SSAP / CATHEDRAL (used by CATH) ===
 
=== SSAP / CATHEDRAL (used by CATH) ===
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[http://v3-4.cathdb.info/cgi-bin/GetSsapRasmol.pl SSAP]
 
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=== Topmatch ===
 
=== Topmatch ===
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[https://topmatch.services.came.sbg.ac.at/ topmatch]
 
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Revision as of 11:18, 29 May 2013

Summary

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Explore structural alignments

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Dataset generation

Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase)

  • reference structure of PAH: 2PAH (96,41% identity)
  • identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI)
  • identical sequence with unfilled binding site: not found anyone
  • low sequence identity: 3LUY (32,2% - no pdb ID under 30%)
  • high sequence identity: pdb ID: 2PHM (89,7%)
  • CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT
  • CA: 2B5U (CATH Code: 1.10.287.620)
  • C: 3BQO (CATH Code: 1.25.40.210)
  • other CATH category: 1V8H (CATH Code: 2.60.40.10)

Pymol

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LGA

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SSAP / CATHEDRAL (used by CATH)

SSAP ...

Topmatch

topmatch ...

SAP or CE

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Modelling scores

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Evaluate sequence alignments

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References

<references/>