Structural Alignments (Phenylketonuria)

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Revision as of 09:55, 30 May 2013 by Waldraffs (talk | contribs) (Modelling scores)

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

CE CE-PDB ...

Modelling scores

<figtable id="rmsd">

RMSD results
Method 1lrm 3luy 2phm 1j8u 2b5u 3bqo 1vh8
LGA-RMSD 0.81 3.30 0.88 0.73 3.07 3.59 3.42
SSAP-RMSD 0.99 18.77 1.24 1.02 39.16 22.39 7.27
Topmatch-Er 0.60 1.98 0.81 0.63 1.21 1.12 3.25
CE-RMSD 0.65 5.13 0.95 0.68 4.06 4.68 5.92
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</figtable>

Evaluate sequence alignments

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References

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