Gaucher Disease: Task 04 - Structural Alignment
From Bioinformatikpedia
Contents
Exploring Structural Alignments
Sequences of Data Set
| Sequence Set | |||
|---|---|---|---|
| PDB ID | Protein name | CATH Superfamily | Category |
| 1ogs | Glucocerebrosidase | Glycosidases (3.20.20.80) | unfilled binding sites (reference structure) |
| 2xwd | Glucocerebrosidase | Glycosidases (3.20.20.80) | filled binding sites |
| 2nsx | Glucocerebrosidase | Glycosidases (3.20.20.80) | filled binding sites |
| 2nt1 | Glucocerebrosidase at neutral pH | Glycosidases (3.20.20.80) | Sequence identity >60% |
| 2f7k* | Pyridoxal kinase | Hydroxyethylthiazole kinase -like domain (3.40.1190.20) | unrelated <30% |
| 1gep | Sulfite reductase | Adolase class I (3.20.20.70) | identical in CAT |
| 2isb | Fumarase of FUM-1 from Archaeoglobus Fulgidus | Fumarase (3.20.130.10) | identical in CA |
| 2djf | Human dipeptidyl peptidase I (in complex) | Cysteine proteinases (3.90.70.10) | identical in C |
| 2qgu | Phospholipid-binding protein from Ralstonia solanacearum (in complex) | Phospholipid-binding protein (1.10.10.640) | different in C |
CATH:
3.20.20 TIM Barrel
3.20 Alpha-Beta Barrel
3 Alpha Beta
1 mostly Alpha
2f7k is not from our set, because we did not have any hits with sequence identity <30% to our reference protein. So we extracted 2f7k randomly from COPS entries with a different L30 group.
Structural alignment methods
| RMSD for Structural Alignments of 1OGS Chain A | ||||
|---|---|---|---|---|
| PDB ID of second molecule | SSAP | LGA | TopMatch | CE |
| 2xwd | 0.89 | 0.62 | ||
| 2nsx | 0.24 | 0.23 | ||
| 2nt1 | 0.68 | 0.5 | ||
| 2f7k | ||||
| 1gep | 4.85 | 3.02 | ||
| 2isb | 14.52 | 2.82 | ||
| 2djf | 9.87 | 2.81 | ||
| 2qgu | 21.03 | 3.59 | ||
