sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2011-11-01
| Name: | Glycine--tRNA ligase alpha subunit |
|---|---|
| ID: | SYGA_CAMJE |
| AC: | Q9PPK3 |
| Organism: | Campylobacter jejuni subsp. jejuni serotype O:2 |
| Reign: | Bacteria |
| TaxID: | 192222 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 89.006 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.176 | 786.375 |
| % Hydrophobic | % Polar |
|---|---|
| 37.34 | 62.66 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 62.6 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 32.0272 | 30.1582 | 3.75548 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| O2G | OG1 | THR- 33 | 2.98 | 162.98 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 58 | 3.02 | 147.73 | H-Bond (Protein Donor) |
| O3A | NH2 | ARG- 58 | 3.02 | 156.72 | H-Bond (Protein Donor) |
| O3A | NH1 | ARG- 58 | 3.37 | 137.81 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 61 | 3.29 | 155.97 | H-Bond (Ligand Donor) |
| N6 | O | LEU- 71 | 2.9 | 120.68 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 71 | 2.95 | 152.95 | H-Bond (Protein Donor) |
| C1' | CE1 | TYR- 74 | 3.92 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 74 | 3.77 | 0 | Aromatic Face/Face |
| O2' | O | GLU- 135 | 3.21 | 153.14 | H-Bond (Ligand Donor) |
| O3' | O | VAL- 136 | 3.41 | 120.42 | H-Bond (Ligand Donor) |
| O1A | NE2 | GLN- 138 | 3.03 | 135.74 | H-Bond (Protein Donor) |
| C5' | CG | GLN- 138 | 4.24 | 0 | Hydrophobic |
| C5' | CG2 | THR- 158 | 4.08 | 0 | Hydrophobic |
| O2' | NE | ARG- 163 | 2.79 | 147.32 | H-Bond (Protein Donor) |
| C2' | CG | ARG- 163 | 4.2 | 0 | Hydrophobic |
