2.700 Å
X-ray
2010-10-02
Name: | 16S rRNA (adenine(1408)-N(1))-methyltransferase |
---|---|
ID: | NPMA_ECOLX |
AC: | A8C927 |
Organism: | Escherichia coli |
Reign: | Bacteria |
TaxID: | 562 |
EC Number: | 2.1.1.180 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 30.877 |
---|---|
Number of residues: | 35 |
Including | |
Standard Amino Acids: | 34 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.760 | 664.875 |
% Hydrophobic | % Polar |
---|---|
49.75 | 50.25 |
According to VolSite |
HET Code: | SAM |
---|---|
Formula: | C15H23N6O5S |
Molecular weight: | 399.445 g/mol |
DrugBank ID: | DB00118 |
Buried Surface Area: | 72.14 % |
Polar Surface area: | 189.77 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 9 |
H-Bond Donors: | 4 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 1 |
Cationic atoms: | 2 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 7 |
X | Y | Z |
---|---|---|
33.6316 | 5.18648 | 44.9311 |
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 | O | GLY- 32 | 3.08 | 156.67 | H-Bond (Ligand Donor) |
O2' | OD2 | ASP- 55 | 2.89 | 146.88 | H-Bond (Ligand Donor) |
O2' | OD1 | ASP- 55 | 3.47 | 150.59 | H-Bond (Ligand Donor) |
N1 | N | ALA- 87 | 2.62 | 165.83 | H-Bond (Protein Donor) |
N6 | OE1 | GLU- 88 | 2.95 | 129.78 | H-Bond (Ligand Donor) |
N | O | LEU- 104 | 2.57 | 127.13 | H-Bond (Ligand Donor) |
CE | CD2 | TRP- 107 | 3.34 | 0 | Hydrophobic |
C5' | CE2 | TRP- 107 | 3.43 | 0 | Hydrophobic |
N6 | OG1 | THR- 109 | 2.91 | 164.51 | H-Bond (Ligand Donor) |
C1' | CD2 | LEU- 110 | 4.15 | 0 | Hydrophobic |
N7 | N | LEU- 110 | 3.33 | 135.85 | H-Bond (Protein Donor) |
CE | CE2 | TRP- 197 | 3.63 | 0 | Hydrophobic |