2.300 Å
X-ray
2006-03-08
| Name: | Poly(A) polymerase catalytic subunit |
|---|---|
| ID: | PAP1_VACCW |
| AC: | P23371 |
| Organism: | Vaccinia virus ) |
| Reign: | Viruses |
| TaxID: | 10254 |
| EC Number: | 2.7.7.19 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 31.841 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | CA CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.538 | 951.750 |
| % Hydrophobic | % Polar |
|---|---|
| 40.07 | 59.93 |
| According to VolSite | |

| HET Code: | AGS |
|---|---|
| Formula: | C10H14N5O12P3S |
| Molecular weight: | 521.231 g/mol |
| DrugBank ID: | DB02930 |
| Buried Surface Area: | 52.51 % |
| Polar Surface area: | 329.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 18.8648 | 13.4809 | 18.9964 |
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 |
| C5' | CE1 | TYR- 186 | 3.84 | 0 | Hydrophobic |
| C4' | CD1 | TYR- 186 | 3.98 | 0 | Hydrophobic |
| O1B | N | SER- 188 | 2.63 | 142.21 | H-Bond (Protein Donor) |
| C2' | CB | ASN- 284 | 4.22 | 0 | Hydrophobic |
| C2' | SD | MET- 288 | 3.96 | 0 | Hydrophobic |
| O2A | NH1 | ARG- 294 | 3.46 | 126.8 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 304 | 2.72 | 135.73 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 304 | 2.72 | 0 | Ionic (Protein Cationic) |
| N6 | OD1 | ASN- 402 | 3.16 | 159.79 | H-Bond (Ligand Donor) |
| N1 | ND2 | ASN- 402 | 3.09 | 161.19 | H-Bond (Protein Donor) |
| O3B | CA | CA- 480 | 2.23 | 0 | Metal Acceptor |
| O3A | CA | CA- 480 | 2.46 | 0 | Metal Acceptor |
| N6 | O | HOH- 492 | 2.95 | 139.31 | H-Bond (Ligand Donor) |