sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-04-23
| Name: | Aspartate carbamoyltransferase regulatory chain |
|---|---|
| ID: | PYRI_METJA |
| AC: | Q58801 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 28 % |
| B | 72 % |
| B-Factor: | 30.839 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 1 |
| Cofactors: | ATP ATP |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.093 | 924.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.07 | 56.93 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 61.29 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 42.722 | 29.466 | 39.5425 |
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 |
| O2' | N | LYS- 10 | 2.85 | 144.18 | H-Bond (Protein Donor) |
| O3G | NE2 | HIS- 20 | 3.17 | 160.65 | H-Bond (Protein Donor) |
| C4' | CG2 | VAL- 47 | 3.94 | 0 | Hydrophobic |
| C1' | CB | VAL- 47 | 4.4 | 0 | Hydrophobic |
| O2G | OG | SER- 49 | 2.59 | 167.22 | H-Bond (Protein Donor) |
| O1G | N | LYS- 50 | 2.78 | 142.7 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 51 | 3.63 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 55 | 2.67 | 156.56 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 55 | 2.6 | 171.54 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 55 | 2.67 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 55 | 2.6 | 0 | Ionic (Protein Cationic) |
| C5' | CD1 | ILE- 57 | 4.5 | 0 | Hydrophobic |
| N6 | N1 | ATP- 402 | 3 | 166.9 | H-Bond (Ligand Donor) |
| N1 | N6 | ATP- 402 | 2.99 | 161.18 | H-Bond (Protein Donor) |
| O3G | ZN | ZN- 502 | 2 | 0 | Metal Acceptor |
| O2B | ZN | ZN- 502 | 2.55 | 0 | Metal Acceptor |
