1.700 Å
X-ray
2007-05-14
Name: | tRNA (adenine(58)-N(1))-methyltransferase TrmI |
---|---|
ID: | TRMI_THET2 |
AC: | Q8GBB2 |
Organism: | Thermus thermophilus |
Reign: | Bacteria |
TaxID: | 262724 |
EC Number: | 2.1.1.220 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 13.125 |
---|---|
Number of residues: | 41 |
Including | |
Standard Amino Acids: | 37 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 4 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.194 | 405.000 |
% Hydrophobic | % Polar |
---|---|
40.00 | 60.00 |
According to VolSite |
HET Code: | SAH |
---|---|
Formula: | C14H20N6O5S |
Molecular weight: | 384.411 g/mol |
DrugBank ID: | DB01752 |
Buried Surface Area: | 71.94 % |
Polar Surface area: | 212.38 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 10 |
H-Bond Donors: | 4 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 1 |
Cationic atoms: | 1 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 7 |
X | Y | Z |
---|---|---|
16.1851 | 40.6778 | -14.631 |
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 |
SD | CB | ALA- 74 | 3.74 | 0 | Hydrophobic |
C3' | CB | ALA- 74 | 4.41 | 0 | Hydrophobic |
N | OG1 | THR- 77 | 2.83 | 124.1 | H-Bond (Ligand Donor) |
O | N | THR- 77 | 2.91 | 156.46 | H-Bond (Protein Donor) |
OXT | N | SER- 104 | 2.8 | 147.32 | H-Bond (Protein Donor) |
OXT | N | GLY- 106 | 3.14 | 158.88 | H-Bond (Protein Donor) |
O | N | LEU- 107 | 2.88 | 160.93 | H-Bond (Protein Donor) |
O3' | OE1 | GLU- 125 | 2.62 | 162.98 | H-Bond (Ligand Donor) |
O3' | OE2 | GLU- 125 | 3.15 | 128.96 | H-Bond (Ligand Donor) |
O2' | OE2 | GLU- 125 | 2.69 | 166.85 | H-Bond (Ligand Donor) |
N3 | N | ALA- 126 | 3.23 | 140.81 | H-Bond (Protein Donor) |
O3' | ND1 | HIS- 130 | 2.79 | 171.76 | H-Bond (Protein Donor) |
N1 | N | LEU- 154 | 3.07 | 167.23 | H-Bond (Protein Donor) |
N6 | OE1 | GLU- 155 | 2.83 | 156.94 | H-Bond (Ligand Donor) |
N | OD2 | ASP- 170 | 2.76 | 163.44 | H-Bond (Ligand Donor) |
N | OD2 | ASP- 170 | 2.76 | 0 | Ionic (Ligand Cationic) |
CG | CB | ASP- 170 | 4.12 | 0 | Hydrophobic |
N | O | HOH- 509 | 2.77 | 164.97 | H-Bond (Ligand Donor) |