2.960 Å
X-ray
2010-04-07
| Name: | Periplasmic serine endoprotease DegP |
|---|---|
| ID: | DEGP_ECOLI |
| AC: | P0C0V0 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 80.701 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.327 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.67 | 58.33 |
| According to VolSite | |

| HET Code: | UNK_UNK_UNK_UNK_UNK |
|---|---|
| Formula: | C15H28N5O5 |
| Molecular weight: | 358.413 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 33.35 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 66.291 | 18.2173 | 29.1303 |
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 |
| O | N | LEU- 265 | 3.07 | 152.45 | H-Bond (Protein Donor) |
| OXT | N | LEU- 265 | 3.44 | 125.17 | H-Bond (Protein Donor) |
| OXT | N | GLY- 266 | 2.99 | 154.8 | H-Bond (Protein Donor) |
| N | O | ILE- 267 | 3 | 172.7 | H-Bond (Ligand Donor) |
| CB | CE | MET- 268 | 4.22 | 0 | Hydrophobic |
| CB | SD | MET- 268 | 4.23 | 0 | Hydrophobic |
| N | O | GLY- 269 | 3.19 | 148.69 | H-Bond (Ligand Donor) |
| O | N | GLY- 269 | 2.91 | 150.72 | H-Bond (Protein Donor) |
| CB | CE2 | PHE- 321 | 3.81 | 0 | Hydrophobic |
| CB | CZ | PHE- 321 | 4.04 | 0 | Hydrophobic |
| CB | CG | ARG- 325 | 4.24 | 0 | Hydrophobic |