2.800 Å
X-ray
2006-07-20
Name: | Diphthine synthase |
---|---|
ID: | DPHB_PYRHO |
AC: | O58456 |
Organism: | Pyrococcus horikoshii |
Reign: | Archaea |
TaxID: | 70601 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 98 % |
B | 2 % |
B-Factor: | 47.531 |
---|---|
Number of residues: | 40 |
Including | |
Standard Amino Acids: | 40 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.129 | 506.250 |
% Hydrophobic | % Polar |
---|---|
42.00 | 58.00 |
According to VolSite |
HET Code: | SAH |
---|---|
Formula: | C14H20N6O5S |
Molecular weight: | 384.411 g/mol |
DrugBank ID: | DB01752 |
Buried Surface Area: | 73.48 % |
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 |
---|---|---|
-14.5622 | -27.9281 | 32.7468 |
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 |
N6 | O | LEU- 10 | 3.49 | 122.68 | H-Bond (Ligand Donor) |
C5' | CB | SER- 37 | 4.32 | 0 | Hydrophobic |
CG | CB | SER- 37 | 3.61 | 0 | Hydrophobic |
O | N | ASP- 87 | 3.29 | 130.92 | H-Bond (Protein Donor) |
N | O | VAL- 90 | 2.8 | 172.29 | H-Bond (Ligand Donor) |
CB | CB | ALA- 91 | 4.33 | 0 | Hydrophobic |
SD | CB | ALA- 91 | 4.34 | 0 | Hydrophobic |
O | OG | SER- 115 | 2.75 | 148.85 | H-Bond (Protein Donor) |
OXT | OG | SER- 115 | 3.17 | 137.18 | H-Bond (Protein Donor) |
CB | CG2 | ILE- 116 | 4.31 | 0 | Hydrophobic |
C1' | CG1 | ILE- 116 | 4.33 | 0 | Hydrophobic |
OXT | N | ILE- 116 | 3.21 | 174.67 | H-Bond (Protein Donor) |
SD | CD1 | PHE- 165 | 3.97 | 0 | Hydrophobic |
C4' | CD1 | PHE- 165 | 3.76 | 0 | Hydrophobic |
O3' | N | LEU- 166 | 2.64 | 135.57 | H-Bond (Protein Donor) |
N6 | O | ALA- 209 | 2.51 | 158.84 | H-Bond (Ligand Donor) |
N1 | N | ALA- 209 | 2.77 | 122.8 | H-Bond (Protein Donor) |
C2' | CB | PRO- 233 | 3.5 | 0 | Hydrophobic |
O3' | O | HIS- 234 | 3.09 | 158.88 | H-Bond (Ligand Donor) |
C1' | CG1 | ILE- 235 | 3.97 | 0 | Hydrophobic |