1.750 Å
X-ray
2013-05-17
Name: | DNA gyrase subunit B |
---|---|
ID: | GYRB_ENTFA |
AC: | Q839Z1 |
Organism: | Enterococcus faecalis |
Reign: | Bacteria |
TaxID: | 226185 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 12.620 |
---|---|
Number of residues: | 29 |
Including | |
Standard Amino Acids: | 27 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.194 | 253.125 |
% Hydrophobic | % Polar |
---|---|
50.67 | 49.33 |
According to VolSite |
HET Code: | 920 |
---|---|
Formula: | C23H26FN8O |
Molecular weight: | 449.504 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 59.2 % |
Polar Surface area: | 119.49 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 7 |
H-Bond Donors: | 3 |
Rings: | 6 |
Aromatic rings: | 4 |
Anionic atoms: | 0 |
Cationic atoms: | 1 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 4 |
X | Y | Z |
---|---|---|
10.1296 | -5.11376 | 14.8355 |
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 |
F31 | CD1 | ILE- 45 | 4 | 0 | Hydrophobic |
C1 | CG2 | ILE- 45 | 3.86 | 0 | Hydrophobic |
C33 | CG2 | ILE- 45 | 4.02 | 0 | Hydrophobic |
C9 | CB | ASN- 48 | 4.33 | 0 | Hydrophobic |
C5 | CB | ASN- 48 | 3.33 | 0 | Hydrophobic |
N29 | OD1 | ASN- 48 | 2.8 | 158.19 | H-Bond (Ligand Donor) |
C33 | CG1 | VAL- 73 | 3.7 | 0 | Hydrophobic |
N7 | OD1 | ASP- 75 | 2.82 | 156.23 | H-Bond (Ligand Donor) |
N32 | OD1 | ASP- 75 | 2.96 | 174.31 | H-Bond (Ligand Donor) |
DuAr | CZ | ARG- 78 | 3.59 | 167.5 | Pi/Cation |
C23 | CG2 | ILE- 80 | 3.88 | 0 | Hydrophobic |
C5 | CD1 | ILE- 80 | 3.76 | 0 | Hydrophobic |
C9 | CG1 | ILE- 80 | 3.37 | 0 | Hydrophobic |
C21 | CG | PRO- 81 | 3.85 | 0 | Hydrophobic |
F31 | CG1 | VAL- 96 | 4.47 | 0 | Hydrophobic |
C5 | CG1 | VAL- 96 | 4.45 | 0 | Hydrophobic |
C30 | CG2 | VAL- 96 | 4.09 | 0 | Hydrophobic |
F31 | CE1 | PHE- 97 | 3.54 | 0 | Hydrophobic |
F31 | CB | SER- 122 | 3.57 | 0 | Hydrophobic |
C33 | CG2 | THR- 167 | 4.3 | 0 | Hydrophobic |
C2 | CG2 | THR- 167 | 3.68 | 0 | Hydrophobic |
C3 | CG2 | THR- 167 | 3.67 | 0 | Hydrophobic |
C33 | CG2 | VAL- 169 | 4.05 | 0 | Hydrophobic |
C1 | CG2 | VAL- 169 | 3.62 | 0 | Hydrophobic |
N13 | O | HOH- 410 | 2.82 | 179.95 | H-Bond (Protein Donor) |