2.050 Å
X-ray
2010-03-01
Name: | DNA-directed DNA polymerase |
---|---|
ID: | DPOL_BPR69 |
AC: | Q38087 |
Organism: | Enterobacteria phage RB69 |
Reign: | Viruses |
TaxID: | 12353 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 5.305 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 26 |
Non Standard Amino Acids: | 2 |
Water Molecules: | 0 |
Cofactors: | |
Metals: | CA CA |
Ligandability | Volume (Å3) |
---|---|
0.647 | 1221.750 |
% Hydrophobic | % Polar |
---|---|
32.87 | 67.13 |
According to VolSite |
HET Code: | CTP |
---|---|
Formula: | C9H12N3O14P3 |
Molecular weight: | 479.125 g/mol |
DrugBank ID: | DB02431 |
Buried Surface Area: | 48.98 % |
Polar Surface area: | 308.95 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 16 |
H-Bond Donors: | 3 |
Rings: | 2 |
Aromatic rings: | 0 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
-1.14039 | 13.3349 | -12.6229 |
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 | N | SER- 414 | 2.85 | 169.45 | H-Bond (Protein Donor) |
O2B | N | LEU- 415 | 2.95 | 167.87 | H-Bond (Protein Donor) |
C4' | CB | LEU- 415 | 4.33 | 0 | Hydrophobic |
C1' | CE2 | TYR- 416 | 4.3 | 0 | Hydrophobic |
C4' | CD1 | TYR- 416 | 4.32 | 0 | Hydrophobic |
C2' | CG | TYR- 416 | 3.7 | 0 | Hydrophobic |
O3' | N | TYR- 416 | 2.94 | 172.66 | H-Bond (Protein Donor) |
O2G | CZ | ARG- 482 | 3.86 | 0 | Ionic (Protein Cationic) |
O3G | CZ | ARG- 482 | 3.47 | 0 | Ionic (Protein Cationic) |
O2G | NH1 | ARG- 482 | 3.02 | 170.09 | H-Bond (Protein Donor) |
O3G | NH2 | ARG- 482 | 2.54 | 172.23 | H-Bond (Protein Donor) |
O1A | NZ | LYS- 560 | 3.22 | 170.86 | H-Bond (Protein Donor) |
O1A | NZ | LYS- 560 | 3.22 | 0 | Ionic (Protein Cationic) |
O3G | NZ | LYS- 560 | 3.59 | 0 | Ionic (Protein Cationic) |
O1B | ND2 | ASN- 564 | 3.37 | 154.01 | H-Bond (Protein Donor) |
C4' | CG2 | THR- 622 | 3.8 | 0 | Hydrophobic |
C5' | CB | ASP- 623 | 4.34 | 0 | Hydrophobic |
O2A | CA | CA- 905 | 2.42 | 0 | Metal Acceptor |
O2B | CA | CA- 905 | 2.51 | 0 | Metal Acceptor |
O1G | CA | CA- 905 | 2.32 | 0 | Metal Acceptor |
O2A | CA | CA- 907 | 2.79 | 0 | Metal Acceptor |