2.600 Å
X-ray
2008-03-04
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: | 57.115 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 28 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.326 | 273.375 |
% Hydrophobic | % Polar |
---|---|
55.56 | 44.44 |
According to VolSite |
HET Code: | GMP |
---|---|
Formula: | C10H13N5O5 |
Molecular weight: | 283.241 g/mol |
DrugBank ID: | DB02857 |
Buried Surface Area: | 69.53 % |
Polar Surface area: | 155.22 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 8 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 0 |
Cationic atoms: | 0 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 2 |
X | Y | Z |
---|---|---|
7.7023 | 7.10565 | 55.6009 |
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 |
C4' | CB | SER- 36 | 3.97 | 0 | Hydrophobic |
C1' | CB | SER- 36 | 3.79 | 0 | Hydrophobic |
C5' | CZ | PHE- 38 | 4.46 | 0 | Hydrophobic |
C1' | CE2 | PHE- 38 | 4.49 | 0 | Hydrophobic |
C5' | CD | ARG- 59 | 4.23 | 0 | Hydrophobic |
N7 | N | MET- 85 | 3.05 | 157.76 | H-Bond (Protein Donor) |
O3' | OD1 | ASP- 95 | 3.06 | 153.18 | H-Bond (Ligand Donor) |
O3' | OD2 | ASP- 95 | 2.79 | 138.59 | H-Bond (Ligand Donor) |
O2' | OD1 | ASP- 95 | 2.58 | 167.8 | H-Bond (Ligand Donor) |
O2' | OD2 | ASP- 95 | 3.26 | 127.66 | H-Bond (Ligand Donor) |
C2' | CZ | PHE- 370 | 4.41 | 0 | Hydrophobic |
C2' | CD | LYS- 374 | 4.33 | 0 | Hydrophobic |
N1 | O | LYS- 378 | 2.81 | 157.41 | H-Bond (Ligand Donor) |
N2 | O | LYS- 378 | 3.19 | 137.38 | H-Bond (Ligand Donor) |
O6 | N | ILE- 380 | 2.95 | 169.93 | H-Bond (Protein Donor) |