sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2006-12-17
| Name: | Type II secretion system protein (GspE-2) |
|---|---|
| ID: | O29598_ARCFU |
| AC: | O29598 |
| Organism: | Archaeoglobus fulgidus |
| Reign: | Archaea |
| TaxID: | 224325 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| 2 | 100 % |
| B-Factor: | 38.830 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.996 | 1167.750 |
| % Hydrophobic | % Polar |
|---|---|
| 38.15 | 61.85 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.62 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 1.87148 | 38.1873 | 178.285 |
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 |
| O3G | CZ | ARG- 208 | 3.93 | 0 | Ionic (Protein Cationic) |
| O2G | CZ | ARG- 227 | 3.86 | 0 | Ionic (Protein Cationic) |
| O2G | NH1 | ARG- 227 | 2.86 | 131.53 | H-Bond (Protein Donor) |
| O3' | O | LYS- 228 | 3.22 | 159.71 | H-Bond (Ligand Donor) |
| O2' | OG1 | THR- 230 | 2.83 | 165.03 | H-Bond (Protein Donor) |
| O3G | OG1 | THR- 269 | 3.4 | 142.15 | H-Bond (Protein Donor) |
| O3G | N | ALA- 270 | 3.08 | 126.1 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 273 | 3.36 | 143.46 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 273 | 3.32 | 127.81 | H-Bond (Protein Donor) |
| O2B | N | LYS- 273 | 2.71 | 153.41 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 273 | 3.27 | 145 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 273 | 3.36 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 273 | 3.32 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 273 | 3.27 | 0 | Ionic (Protein Cationic) |
| O1B | N | THR- 274 | 2.98 | 156.73 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 275 | 3.02 | 159.05 | H-Bond (Protein Donor) |
| O1A | N | THR- 275 | 3.05 | 171.48 | H-Bond (Protein Donor) |
| O1G | MG | MG- 512 | 2.76 | 0 | Metal Acceptor |
| O1B | MG | MG- 512 | 1.98 | 0 | Metal Acceptor |
