2.700 Å
X-ray
2005-05-23
Name: | Methionine--tRNA ligase |
---|---|
ID: | SYM_AQUAE |
AC: | O67298 |
Organism: | Aquifex aeolicus |
Reign: | Bacteria |
TaxID: | 224324 |
EC Number: | 6.1.1.10 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 23.311 |
---|---|
Number of residues: | 36 |
Including | |
Standard Amino Acids: | 36 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.805 | 688.500 |
% Hydrophobic | % Polar |
---|---|
50.49 | 49.51 |
According to VolSite |
HET Code: | MSP |
---|---|
Formula: | C15H27N7O7S2 |
Molecular weight: | 481.548 g/mol |
DrugBank ID: | DB02229 |
Buried Surface Area: | 78.79 % |
Polar Surface area: | 254.78 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 10 |
H-Bond Donors: | 6 |
Rings: | 3 |
Aromatic rings: | 0 |
Anionic atoms: | 1 |
Cationic atoms: | 3 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 9 |
X | Y | Z |
---|---|---|
11.6165 | 20.263 | 24.7303 |
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 |
CB | CB | PRO- 12 | 4.05 | 0 | Hydrophobic |
SD | CB | PRO- 12 | 3.78 | 0 | Hydrophobic |
C4' | CG | PRO- 12 | 4.4 | 0 | Hydrophobic |
N2 | O | ILE- 13 | 2.89 | 166.97 | H-Bond (Ligand Donor) |
CE | CG1 | ILE- 13 | 3.48 | 0 | Hydrophobic |
CG | CG1 | ILE- 13 | 3.62 | 0 | Hydrophobic |
C4' | CE2 | TYR- 14 | 3.42 | 0 | Hydrophobic |
O1S | N | TYR- 15 | 3 | 161.32 | H-Bond (Protein Donor) |
N2 | OD2 | ASP- 52 | 2.94 | 149.7 | H-Bond (Ligand Donor) |
N2 | OD2 | ASP- 52 | 2.94 | 0 | Ionic (Ligand Cationic) |
CG | CH2 | TRP- 230 | 3.47 | 0 | Hydrophobic |
SD | CZ3 | TRP- 230 | 3.98 | 0 | Hydrophobic |
CG | CB | ALA- 233 | 4.25 | 0 | Hydrophobic |
CE | CB | ALA- 233 | 3.86 | 0 | Hydrophobic |
CE | CD2 | LEU- 234 | 4.15 | 0 | Hydrophobic |
CE | CZ | TYR- 237 | 4.01 | 0 | Hydrophobic |
O3' | N | GLY- 257 | 3.15 | 137.86 | H-Bond (Protein Donor) |
O2' | OD1 | ASP- 259 | 2.84 | 165.33 | H-Bond (Ligand Donor) |
CB | CD1 | ILE- 260 | 4.04 | 0 | Hydrophobic |
C3' | CD1 | ILE- 260 | 4.21 | 0 | Hydrophobic |
DuAr | DuAr | TRP- 288 | 3.65 | 0 | Aromatic Face/Face |
C2' | CZ3 | TRP- 288 | 3.56 | 0 | Hydrophobic |
N6 | O | TRP- 289 | 3.18 | 163.71 | H-Bond (Ligand Donor) |
N1 | N | TRP- 289 | 2.86 | 153.15 | H-Bond (Protein Donor) |