2.850 Å
X-ray
2002-12-30
Name: | Proline--tRNA ligase |
---|---|
ID: | SYP_METTH |
AC: | O26708 |
Organism: | Methanothermobacter thermautotrophicus |
Reign: | Archaea |
TaxID: | 187420 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 59.295 |
---|---|
Number of residues: | 42 |
Including | |
Standard Amino Acids: | 41 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.067 | 580.500 |
% Hydrophobic | % Polar |
---|---|
31.40 | 68.60 |
According to VolSite |
HET Code: | A5A |
---|---|
Formula: | C13H19N7O7S |
Molecular weight: | 417.398 g/mol |
DrugBank ID: | DB03376 |
Buried Surface Area: | 74.86 % |
Polar Surface area: | 229.86 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 11 |
H-Bond Donors: | 4 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 1 |
Cationic atoms: | 1 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 6 |
X | Y | Z |
---|---|---|
-31.5175 | -81.7609 | -35.9539 |
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 |
N | OG1 | THR- 117 | 2.95 | 142.87 | H-Bond (Ligand Donor) |
N | OE1 | GLU- 119 | 3.8 | 0 | Ionic (Ligand Cationic) |
N | OE2 | GLU- 119 | 2.61 | 0 | Ionic (Ligand Cationic) |
O | NH2 | ARG- 148 | 3.18 | 135.01 | H-Bond (Protein Donor) |
O1S | NH1 | ARG- 148 | 3.17 | 140.17 | H-Bond (Protein Donor) |
O1S | NH2 | ARG- 148 | 3.14 | 141.29 | H-Bond (Protein Donor) |
N6 | OE1 | GLU- 150 | 3.08 | 131.55 | H-Bond (Ligand Donor) |
N6 | O | VAL- 160 | 3.33 | 137.3 | H-Bond (Ligand Donor) |
N1 | N | VAL- 160 | 3.31 | 163.46 | H-Bond (Protein Donor) |
C5' | CE1 | PHE- 166 | 3.91 | 0 | Hydrophobic |
O3' | OE1 | GLN- 232 | 3.23 | 137.8 | H-Bond (Ligand Donor) |
O2' | O | GLN- 232 | 2.85 | 152.8 | H-Bond (Ligand Donor) |
N3S | OG1 | THR- 235 | 3.48 | 127.95 | H-Bond (Ligand Donor) |
O2S | OG1 | THR- 235 | 3.01 | 162.45 | H-Bond (Protein Donor) |
C3' | CG2 | THR- 235 | 4.33 | 0 | Hydrophobic |
N3S | NE2 | HIS- 237 | 3.25 | 151.55 | H-Bond (Ligand Donor) |
CB | SG | CYS- 265 | 3.94 | 0 | Hydrophobic |
C1' | CB | SER- 269 | 3.6 | 0 | Hydrophobic |
N3 | OG | SER- 269 | 2.77 | 173.4 | H-Bond (Protein Donor) |
C2' | CD | ARG- 271 | 3.93 | 0 | Hydrophobic |
N7 | O | HOH- 487 | 2.74 | 160.71 | H-Bond (Protein Donor) |