Table 2.
Bioinformatics Results from HKU9 C Structure‐Based Alignment and Protein Function Prediction
| Identifier | Protein Name | RMSD | %ID | ||
|---|---|---|---|---|---|
| A | |||||
| TM‐Align a | PDB ID: 2KAF | SARS nsp3 C domain | 1.66 | 18 | |
| PDB ID: 4YPT | MHV nsp3 domain | 2.21 | 15 | ||
| PDB ID: 1KAF | Phage T4 MotA | 2.84 | 7 | ||
| PDB ID: 1YB3 | P. furiosus 178653–001 | 3.12 | 1 | ||
| DALI b | PDB ID: 2KAF | SARS nsp3 C domain | 1.8 | 18 | |
| PDB ID: 4YPT | MHV nsp3 domain | 2.3 | 15 | ||
| PDB ID: 1KAF | Phage T4 MotA | 2.7 | 9 | ||
| PDB ID: 4HS5 | P. ingrahamii FTXN | 2.8 | 9 | ||
| PDB ID: 3T3X | Friedreich's Ataxia FTXN | 2.9 | 6 | ||
| PDB ID: 1YB3 | P. furiosus 178653–001 | 3.3 | 1 | ||
| Server Prediction | Structurally Similar Proteins | Alignment Scoresd | ||||
|---|---|---|---|---|---|---|
| Ligand | Binding Sitec | C | BS | |||
| B | ||||||
| COFACTOR | DNA | β | Ring 1B/Bmi1/UbcH5c PRC1 (4R8P) | 0.01 | 0.86 | |
| Peptide | α/β | Glycyl‐tRNA Synthetase (1ATI) | 0.01 | 0.77 | ||
| Cyanocobalamin (Vitamin B12) | CF | Glycerol Dehydratase (1MMF) | 0.01 | 0.20 | ||
| ATP | β | Human Glycyl‐tRNA synthetase (2ZT7) | 0.01 | 0.15 | ||
| C | ||||||
| COACH |
Calcium ions Zinc ions |
α α |
E. coli ROM variant (1F4M) Acyl Carrier Protein (2QNW) |
0.12 0.11 |
||
| “GAANDENY” | CF | AAA+ delivery protein (1OU8) | 0.09 | |||
| “QRKWYPLRP” | CF | KnI1/NsI1 complex (4NF9) | 0.05 | |||
| Peptide | α/β | Glycyl‐tRNA Synthetase (1ATI) | 0.04 | |||
| DNA | β | Ring 1B/Bmi1/UbcH5c PRC1 (4R8P) | 0.02 | |||
| Serotonin | α | AM182 Serotonin Complex (3BRN) | 0.02 | |||
| TM‐Site | Zinc(II) ions | α | Ferric Enterobactin (2CHU) | 0.37 | ||
| Apcin | β | Cdc20 (4N14) | 0.18 | |||
| FINDSITE | “GAANDENY” | CF | AAA+ delivery protein (1OU8) | 0.27 | ||
| N‐acetyl‐mannosamine | α | L‐Ficolin protein (2J0G) | 0.13 | |||
| Serotonin | α | AM182 Serotonin Complex (3BRN) | 0.06 | |||
TM‐Align[50] scales structure similarity to protein templates from residue‐specific alignment.
DALI[51] server uses structure‐based templates to provide matches in structure and function.
Predicted binding regions of the HKU9 C protein are described: residues from the α‐helices (α), residues from the solvent‐accessible β‐sheet (β), and the conserved polar face containing the Arg‐Asp‐Trp and Lys‐Arg‐Gly motif (CF).
The confidence score (C‐score) is used to evaluate the reliability of the prediction. The binding site score (BS‐score) evaluates how significant is the match between the predicted binding site and the template binding site. Alignment score values range from 0 to 1, with higher values having greater significance.