2.230 Å
X-ray
2007-12-17
Name: | Geranylgeranyl pyrophosphate synthase |
---|---|
ID: | GGPPS_YEAST |
AC: | Q12051 |
Organism: | Saccharomyces cerevisiae |
Reign: | Eukaryota |
TaxID: | 559292 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 42.440 |
---|---|
Number of residues: | 38 |
Including | |
Standard Amino Acids: | 35 |
Non Standard Amino Acids: | 2 |
Water Molecules: | 1 |
Cofactors: | |
Metals: | MG MG |
Ligandability | Volume (Å3) |
---|---|
1.053 | 580.500 |
% Hydrophobic | % Polar |
---|---|
61.63 | 38.37 |
According to VolSite |
HET Code: | B71 |
---|---|
Formula: | C17H28NO7P2 |
Molecular weight: | 420.354 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 61.21 % |
Polar Surface area: | 159.1 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 7 |
H-Bond Donors: | 0 |
Rings: | 1 |
Aromatic rings: | 1 |
Anionic atoms: | 4 |
Cationic atoms: | 1 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 14 |
X | Y | Z |
---|---|---|
30.9664 | 48.2998 | 8.53081 |
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 |
CAM | CG | ARG- 44 | 3.99 | 0 | Hydrophobic |
CAA | CD2 | LEU- 47 | 3.73 | 0 | Hydrophobic |
CAA | CG1 | ILE- 48 | 4.02 | 0 | Hydrophobic |
CAM | CG1 | VAL- 69 | 3.56 | 0 | Hydrophobic |
OAF | NH2 | ARG- 89 | 2.85 | 136.01 | H-Bond (Protein Donor) |
OAC | NH2 | ARG- 89 | 3.43 | 127.39 | H-Bond (Protein Donor) |
OAC | NH1 | ARG- 89 | 2.65 | 169 | H-Bond (Protein Donor) |
OAF | CZ | ARG- 89 | 3.69 | 0 | Ionic (Protein Cationic) |
OAC | CZ | ARG- 89 | 3.49 | 0 | Ionic (Protein Cationic) |
CAI | CD1 | LEU- 143 | 3.6 | 0 | Hydrophobic |
OAB | NZ | LYS- 174 | 3.06 | 159.91 | H-Bond (Protein Donor) |
OAB | NZ | LYS- 174 | 3.06 | 0 | Ionic (Protein Cationic) |
CAH | CG | LYS- 174 | 3.57 | 0 | Hydrophobic |
CAT | CG2 | THR- 175 | 3.6 | 0 | Hydrophobic |
CAL | CD1 | PHE- 179 | 4.25 | 0 | Hydrophobic |
CAQ | CZ | PHE- 179 | 3.27 | 0 | Hydrophobic |
CAR | CE2 | PHE- 179 | 3.99 | 0 | Hydrophobic |
CAA | CG2 | THR- 182 | 3.44 | 0 | Hydrophobic |
CAL | CB | THR- 182 | 4.13 | 0 | Hydrophobic |
CAQ | CZ | TYR- 210 | 3.92 | 0 | Hydrophobic |
CAR | CE2 | TYR- 210 | 3.34 | 0 | Hydrophobic |
OAD | NE2 | GLN- 211 | 3.43 | 142.85 | H-Bond (Protein Donor) |
OAG | OD1 | ASP- 214 | 2.82 | 156.67 | H-Bond (Protein Donor) |
OAD | OD1 | ASP- 214 | 3.03 | 129.07 | H-Bond (Protein Donor) |
OAG | NZ | LYS- 238 | 3.92 | 0 | Ionic (Protein Cationic) |
OAE | NZ | LYS- 238 | 3.35 | 0 | Ionic (Protein Cationic) |
OAE | NZ | LYS- 238 | 3.35 | 127.34 | H-Bond (Protein Donor) |
OAE | MG | MG- 1301 | 2.23 | 0 | Metal Acceptor |
OAF | MG | MG- 1302 | 2.15 | 0 | Metal Acceptor |
OAE | MG | MG- 1302 | 2.14 | 0 | Metal Acceptor |