2.100 Å
X-ray
2007-12-05
| Name: | Ribonuclease J |
|---|---|
| ID: | RNJ_THET2 |
| AC: | Q72JJ7 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 262724 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.104 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.868 | 1022.625 |
| % Hydrophobic | % Polar |
|---|---|
| 36.30 | 63.70 |
| According to VolSite | |

| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.67 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 12.1503 | 35.8538 | 36.3558 |
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 |
| C4' | CG2 | ILE- 21 | 3.97 | 0 | Hydrophobic |
| C5' | CG2 | THR- 206 | 4.34 | 0 | Hydrophobic |
| C2' | CZ | PHE- 240 | 4.22 | 0 | Hydrophobic |
| O2' | O | SER- 340 | 2.87 | 163.92 | H-Bond (Ligand Donor) |
| C3' | CB | SER- 340 | 4.4 | 0 | Hydrophobic |
| O3P | OG | SER- 340 | 2.62 | 163.62 | H-Bond (Protein Donor) |
| O3' | O | PRO- 341 | 2.82 | 167.44 | H-Bond (Ligand Donor) |
| C1' | CD1 | ILE- 342 | 4.33 | 0 | Hydrophobic |
| O3P | NE2 | HIS- 372 | 2.75 | 169.86 | H-Bond (Protein Donor) |
| O1P | N | GLY- 375 | 3.01 | 148.57 | H-Bond (Protein Donor) |