2.010 Å
X-ray
2008-06-26
| Name: | Glucose 1-dehydrogenase |
|---|---|
| ID: | GLCDH_HALMT |
| AC: | Q977U7 |
| Organism: | Haloferax mediterranei |
| Reign: | Archaea |
| TaxID: | 523841 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.040 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.778 | 567.000 |
| % Hydrophobic | % Polar |
|---|---|
| 46.43 | 53.57 |
| According to VolSite | |

| HET Code: | NDP |
|---|---|
| Formula: | C21H26N7O17P3 |
| Molecular weight: | 741.389 g/mol |
| DrugBank ID: | DB02338 |
| Buried Surface Area: | 56.68 % |
| Polar Surface area: | 404.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -0.679604 | 26.3101 | 18.8553 |
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 |
| C4N | CG2 | ILE- 154 | 3.74 | 0 | Hydrophobic |
| C5N | CD2 | LEU- 184 | 3.93 | 0 | Hydrophobic |
| O2X | NE | ARG- 207 | 3.08 | 144.74 | H-Bond (Protein Donor) |
| O2X | NH2 | ARG- 207 | 2.93 | 150.57 | H-Bond (Protein Donor) |
| O2X | CZ | ARG- 207 | 3.44 | 0 | Ionic (Protein Cationic) |
| O1X | CZ | ARG- 208 | 3.89 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 208 | 3.95 | 0 | Ionic (Protein Cationic) |
| O1X | NH2 | ARG- 208 | 3.14 | 161.71 | H-Bond (Protein Donor) |
| O3X | NE | ARG- 208 | 2.96 | 162.18 | H-Bond (Protein Donor) |
| N1A | OG | SER- 228 | 2.69 | 157.99 | H-Bond (Protein Donor) |
| C5D | CB | ALA- 249 | 3.94 | 0 | Hydrophobic |
| C1B | CG2 | THR- 250 | 4.27 | 0 | Hydrophobic |
| N7N | O | LEU- 272 | 3.03 | 172.49 | H-Bond (Ligand Donor) |
| N7N | O | SER- 301 | 2.83 | 137.65 | H-Bond (Ligand Donor) |
| O7N | N | ASN- 303 | 2.87 | 161.12 | H-Bond (Protein Donor) |