1.600 Å
X-ray
2004-04-02
| Name: | MutT/nudix family protein |
|---|---|
| ID: | Q9RVK2_DEIRA |
| AC: | Q9RVK2 |
| Organism: | Deinococcus radiodurans |
| Reign: | Bacteria |
| TaxID: | 243230 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 81 % |
| B | 19 % |
| B-Factor: | 24.381 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.119 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 46.67 | 53.33 |
| According to VolSite | |

| HET Code: | GNP |
|---|---|
| Formula: | C10H13N6O13P3 |
| Molecular weight: | 518.164 g/mol |
| DrugBank ID: | DB02082 |
| Buried Surface Area: | 58.6 % |
| Polar Surface area: | 338.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 46.661 | 1.11509 | 27.5423 |
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 |
| C3' | CE | MET- 1 | 3.87 | 0 | Hydrophobic |
| C4' | CG | GLU- 2 | 3.52 | 0 | Hydrophobic |
| C1' | CB | ASP- 4 | 3.99 | 0 | Hydrophobic |
| O3' | NH2 | ARG- 6 | 3.27 | 164.42 | H-Bond (Protein Donor) |
| O2B | OG | SER- 49 | 2.9 | 135.84 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 87 | 3.86 | 0 | Aromatic Face/Face |
| C2' | CZ | PHE- 87 | 3.26 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 89 | 2.87 | 144.7 | H-Bond (Protein Donor) |
| C3' | CD1 | ILE- 93 | 3.68 | 0 | Hydrophobic |
| O1B | NH1 | ARG- 95 | 2.93 | 126.81 | H-Bond (Protein Donor) |