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 |
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) |