2.590 Å
X-ray
2007-05-22
Name: | Dodecin |
---|---|
ID: | DODEC_THET8 |
AC: | Q5SIE3 |
Organism: | Thermus thermophilus |
Reign: | Bacteria |
TaxID: | 300852 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
C | 4 % |
F | 36 % |
J | 36 % |
K | 25 % |
B-Factor: | 34.281 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 26 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 1 |
Cofactors: | FMN |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.284 | 641.250 |
% Hydrophobic | % Polar |
---|---|
39.47 | 60.53 |
According to VolSite |
HET Code: | FMN |
---|---|
Formula: | C17H19N4O9P |
Molecular weight: | 454.328 g/mol |
DrugBank ID: | DB03247 |
Buried Surface Area: | 58.27 % |
Polar Surface area: | 217.05 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 12 |
H-Bond Donors: | 4 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 7 |
X | Y | Z |
---|---|---|
3.56484 | -0.602323 | -31.0194 |
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 |
O2P | NZ | LYS- 3 | 3.12 | 167.92 | H-Bond (Protein Donor) |
O2P | NZ | LYS- 3 | 3.12 | 0 | Ionic (Protein Cationic) |
C8M | CD2 | TYR- 5 | 4.27 | 0 | Hydrophobic |
C5' | CZ | TYR- 5 | 4.07 | 0 | Hydrophobic |
C7M | CG1 | VAL- 11 | 3.99 | 0 | Hydrophobic |
C8M | CG1 | VAL- 11 | 3.73 | 0 | Hydrophobic |
C2' | CB | ASP- 37 | 4.46 | 0 | Hydrophobic |
C7M | CZ2 | TRP- 38 | 4.39 | 0 | Hydrophobic |
C8M | CH2 | TRP- 38 | 4.11 | 0 | Hydrophobic |
C2' | CE3 | TRP- 38 | 4.27 | 0 | Hydrophobic |
DuAr | DuAr | TRP- 38 | 3.91 | 0 | Aromatic Face/Face |
O2 | NE2 | GLN- 57 | 2.72 | 149.33 | H-Bond (Protein Donor) |
N3 | OE1 | GLN- 57 | 2.55 | 162.24 | H-Bond (Ligand Donor) |
C7M | CB | GLN- 57 | 4.43 | 0 | Hydrophobic |
C8M | CG | GLN- 57 | 3.96 | 0 | Hydrophobic |
C7M | CG2 | VAL- 59 | 3.94 | 0 | Hydrophobic |