# Gaucher Disease: Task 05 - Lab Journal

**This page is still under construction**

## Contents

## Calculation of models

### Structures set

We assembled the following structures in task 4, now we divide them into two groups: at > 60% and at < 30% sequence identity to our template protein, P04062 (536 aa long). PIDE was calculated as follows:

- first we aligned the two fasta sequences from PDB with ClustalW
- then calculated the PIDE (pairwise sequence identity) using SIAS with default options

Selected structures for single-template modelling are written in bold.

Homologous structures to P04062 | ||
---|---|---|

PDB ID | PIDE with target (%) | Length (aa) |

High PIDE | ||

2XWD_A | 91.51 | 505 |

2NSX_A | 92.53 | 497 |

2NT1_A | 92.53 | 497 |

Low PIDE | ||

2GEP_A | 10.74 | 497 |

2F7K_A | 8.95 | 327 |

2QGU | 5.59 | 211 |

2ISB_A | 5.59 | 192 |

2DJF_A | 3.17 | 119 |

2DJF_B | 2.98 | 164 |

2DJF_C | 4.47 | 69 |

As the PIDE with P04062 in the low-PIDE group we have selected in task 4 is too low and 10.74% PIDE with 2GEP_A was not enough for Swissmodel to align the sequences, we looked again at the found hit list in task 2 (HHblits, 2 iterations against Uniprot20 followed by one iteration against pdb_full with E-value cutoff 10E-10). The set of structures finally used is:

Homologous structures to P04062 | ||||
---|---|---|---|---|

PDB ID | PIDE of alignment with target (%) | Length (aa) | Aligned columns (aa) | Query coverage |

High PIDE | ||||

3KE0_A | 100 | 497 | 496 | 41-536 |

2XWD_A | 100 | 505 | 497 | 40-536 |

2WKL_A | 100 | 497 | 496 | 41-536 |

2NSX_A | 100 | 497 | 496 | 41-536 |

Low PIDE | ||||

2WNW_A | 29 | 447 | 440 | 75-534 |

1VFF_A | 22 | 423 | 98 | 151-228 |

3II1_A | 20 | 535 | 84 | 452-514 |

### Modeller

TODO: execution scripts

### Swissmodel

### iTasser

### Pymol

We visualized all created models with Pymol. For this we aligned each model with the reference structure, 1OGS, and calculated the RMSD between the corresponding C_alpha atoms like in task 4:

align 1ogs_A and resi 1-497 and name ca, P04062.model and resi 1-n and name ca

where "P04062.model" is the name of the model and "n" its last residue.