1.600 Å
X-ray
2005-05-13
Name: | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase |
---|---|
ID: | Q8DQ16_STRR6 |
AC: | Q8DQ16 |
Organism: | Streptococcus pneumoniae |
Reign: | Bacteria |
TaxID: | 171101 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
E | 11 % |
F | 89 % |
B-Factor: | 12.594 |
---|---|
Number of residues: | 38 |
Including | |
Standard Amino Acids: | 36 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.024 | 297.000 |
% Hydrophobic | % Polar |
---|---|
65.91 | 34.09 |
According to VolSite |
HET Code: | MTM |
---|---|
Formula: | C12H22N5O2S |
Molecular weight: | 300.400 g/mol |
DrugBank ID: | DB02158 |
Buried Surface Area: | 82.17 % |
Polar Surface area: | 151.8 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 3 |
H-Bond Donors: | 7 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 0 |
Cationic atoms: | 3 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 3 |
X | Y | Z |
---|---|---|
18.3861 | 27.8112 | 48.7701 |
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 |
C3' | CG2 | ILE- 50 | 3.9 | 0 | Hydrophobic |
CS | CD1 | ILE- 50 | 3.78 | 0 | Hydrophobic |
CS | CE2 | PHE- 105 | 3.69 | 0 | Hydrophobic |
S5' | CB | ALA- 113 | 4.41 | 0 | Hydrophobic |
C5 | CE2 | PHE- 151 | 3.37 | 0 | Hydrophobic |
C5' | CD2 | PHE- 151 | 3.63 | 0 | Hydrophobic |
N6 | O | VAL- 152 | 2.97 | 140.56 | H-Bond (Ligand Donor) |
N1 | N | VAL- 152 | 2.91 | 150.23 | H-Bond (Protein Donor) |
C2' | CB | GLU- 172 | 4.06 | 0 | Hydrophobic |
C2' | CB | MET- 173 | 3.88 | 0 | Hydrophobic |
C3' | SD | MET- 173 | 3.79 | 0 | Hydrophobic |
S5' | SD | MET- 173 | 3.65 | 0 | Hydrophobic |
O2' | N | MET- 173 | 2.92 | 160.44 | H-Bond (Protein Donor) |
O2' | OE2 | GLU- 174 | 2.6 | 142.37 | H-Bond (Ligand Donor) |
O3' | OE2 | GLU- 174 | 3.09 | 143.99 | H-Bond (Ligand Donor) |
O3' | OE1 | GLU- 174 | 2.64 | 150.04 | H-Bond (Ligand Donor) |
O2' | NH1 | ARG- 193 | 3.02 | 152.92 | H-Bond (Protein Donor) |
N7 | OD2 | ASP- 197 | 2.61 | 154.46 | H-Bond (Ligand Donor) |
N6 | OD1 | ASP- 197 | 2.84 | 163.36 | H-Bond (Ligand Donor) |
CS | CE2 | PHE- 207 | 3.97 | 0 | Hydrophobic |
C5' | CE1 | PHE- 207 | 4.4 | 0 | Hydrophobic |