sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2008-08-24
| Name: | ATPase, ParA family |
|---|---|
| ID: | Q8KF94_CHLTE |
| AC: | Q8KF94 |
| Organism: | Chlorobium tepidum |
| Reign: | Bacteria |
| TaxID: | 194439 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 88 % |
| B | 12 % |
| B-Factor: | 36.592 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.007 | 1285.875 |
| % Hydrophobic | % Polar |
|---|---|
| 32.28 | 67.72 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 77.09 % |
| 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 |
|---|---|---|
| 20.7953 | -3.17481 | 53.7028 |
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 |
| O1B | OG | SER- 8 | 2.86 | 152.39 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 10 | 3.44 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 10 | 2.92 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 10 | 2.92 | 153.1 | H-Bond (Protein Donor) |
| O1B | N | GLY- 12 | 3.45 | 127.17 | H-Bond (Protein Donor) |
| O2B | N | GLY- 12 | 2.93 | 162.03 | H-Bond (Protein Donor) |
| O1B | N | GLY- 14 | 2.7 | 152.83 | H-Bond (Protein Donor) |
| O3A | N | GLY- 14 | 3.44 | 129.17 | H-Bond (Protein Donor) |
| O1B | N | GLY- 15 | 2.87 | 148.57 | H-Bond (Protein Donor) |
| O3B | N | SER- 16 | 3.04 | 169.74 | H-Bond (Protein Donor) |
| O2A | N | CYS- 17 | 2.7 | 165.28 | H-Bond (Protein Donor) |
| C2' | CB | CYS- 17 | 4.45 | 0 | Hydrophobic |
| O1A | OH | TYR- 49 | 2.65 | 131.53 | H-Bond (Protein Donor) |
| C3' | CZ | TYR- 49 | 4.31 | 0 | Hydrophobic |
| C2' | CE1 | TYR- 49 | 3.97 | 0 | Hydrophobic |
| O2' | NE2 | GLN- 150 | 3.41 | 123.5 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 177 | 3.01 | 170.35 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 177 | 3.06 | 138.25 | H-Bond (Ligand Donor) |
| O4' | NH2 | ARG- 178 | 3.17 | 151.33 | H-Bond (Protein Donor) |
| N6 | O | PRO- 203 | 2.97 | 159.69 | H-Bond (Ligand Donor) |
| N1 | N | ASP- 205 | 2.77 | 175.79 | H-Bond (Protein Donor) |
| O3G | MG | MG- 244 | 2.33 | 0 | Metal Acceptor |
| O2B | O | HOH- 249 | 2.64 | 174.96 | H-Bond (Protein Donor) |
| O2G | O | HOH- 286 | 2.67 | 144.61 | H-Bond (Protein Donor) |
