Structural Alignments (Phenylketonuria)
From Bioinformatikpedia
Contents
Summary
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Explore structural alignments
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
LGA ...
SSAP / CATHEDRAL (used by CATH)
SSAP
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uses Cβ
TopMatch
TopMatch
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uses Cα
SAP or CE
SAP? ->Error!
->
CE
CE-PDB
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Modelling scores
To compare the different models, the RMSDs (root-mean-square deviation) are compared. In TopMatch the same formular is taken but called Er (root-mean-square error). The RMSD gives the squared distance between corresponding positions of two superimposed proteins in Ångström. The results are shown in <xr id="rmsd"/>. <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 |
</figtable>
- lowest RMSDs: TopMatch
- LGA and CE sometimes the one sometimes the other is better. For very similar structures CE better, otherwise LGA???
- worst/highest RMSDs: SSAP, maybe the Cβ are more distant???
- careful about the sidechains: here always 2pah.A as query is taken and xx.A as target
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Evaluate sequence alignments
Lab journal
<figtable id="model_rmsd">
| LGA and hhsearch results | |||||||
|---|---|---|---|---|---|---|---|
| LGA | hhsearch | ||||||
| pdb | RMSD | LGA_S | LGA_Q | seq_id | probability | e-value | identities(%) |
| 1phz | 0.83 | 90.65 | 32.44 | 99.34 | 100.00 | 6.9e-165 | 92 |
| 1j8u | 0.73 | 90.29 | 35.83 | 99.67 | 100.00 | 3.1e-135 | 100 |
| 2v27 | 1.70 | 62.77 | 12.55 | 96.02 | 100.00 | 3.6e-74 | 32 |
| 2qmx | 3.18 | 7.46 | 1.25 | 4.88 | 98.20 | 1.1e-09 | 36 |
| 3luy | 2.82 | 7.17 | 1.24 | 13.89 | 98.07 | 3.3e-09 | 22 |
| 1qey | 0.64 | 3.65 | 1.63 | 0.00 | 54.00 | 3.4 | 67 |
| 1wyp | 2.67 | 8.43 | 1.37 | 0.00 | 29.42 | 15 | 19 |
| 1a6s | 3.15 | 6.93 | 1.08 | 11.43 | 20.59 | 29 | 36 |
</figtable>
References
<references/>
