2.820 Å
X-ray
2015-06-04
Name: | 2-succinylbenzoate--CoA ligase |
---|---|
ID: | MENE_BACSU |
AC: | P23971 |
Organism: | Bacillus subtilis |
Reign: | Bacteria |
TaxID: | 224308 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 60.328 |
---|---|
Number of residues: | 37 |
Including | |
Standard Amino Acids: | 36 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 0 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.048 | 2740.500 |
% Hydrophobic | % Polar |
---|---|
45.57 | 54.43 |
According to VolSite |
HET Code: | ATP |
---|---|
Formula: | C10H12N5O13P3 |
Molecular weight: | 503.149 g/mol |
DrugBank ID: | DB00171 |
Buried Surface Area: | 64.53 % |
Polar Surface area: | 319.88 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
63.3645 | 155.815 | 13.2242 |
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 |
O3B | N | SER- 153 | 3.37 | 128.24 | H-Bond (Protein Donor) |
O3A | OG | SER- 153 | 2.83 | 167.07 | H-Bond (Protein Donor) |
O3G | N | GLY- 154 | 3.37 | 151.14 | H-Bond (Protein Donor) |
O1B | OG1 | THR- 155 | 2.98 | 166.33 | H-Bond (Protein Donor) |
O1G | OG1 | THR- 156 | 3.22 | 170.32 | H-Bond (Protein Donor) |
O1G | N | THR- 156 | 3.22 | 153.76 | H-Bond (Protein Donor) |
O2G | NZ | LYS- 160 | 3.55 | 0 | Ionic (Protein Cationic) |
O3G | NZ | LYS- 160 | 4 | 0 | Ionic (Protein Cationic) |
C2' | CE1 | TYR- 286 | 4.13 | 0 | Hydrophobic |
C5' | CB | MET- 288 | 3.84 | 0 | Hydrophobic |
C3' | CB | MET- 288 | 4.38 | 0 | Hydrophobic |
O1A | N | THR- 289 | 3.34 | 173.93 | H-Bond (Protein Donor) |
O1A | OG1 | THR- 289 | 3.24 | 160.58 | H-Bond (Protein Donor) |
O3' | OD2 | ASP- 367 | 2.81 | 156.79 | H-Bond (Ligand Donor) |
O3' | OD1 | ASP- 367 | 3.21 | 141.88 | H-Bond (Ligand Donor) |
O2' | OD2 | ASP- 367 | 3.2 | 135.4 | H-Bond (Ligand Donor) |
O2' | OD1 | ASP- 367 | 2.79 | 152.43 | H-Bond (Ligand Donor) |
O1B | NH1 | ARG- 382 | 3.4 | 121.47 | H-Bond (Protein Donor) |
O1B | NH2 | ARG- 382 | 2.77 | 138.49 | H-Bond (Protein Donor) |
O1B | CZ | ARG- 382 | 3.46 | 0 | Ionic (Protein Cationic) |
O2A | NZ | LYS- 471 | 3.59 | 0 | Ionic (Protein Cationic) |
O2G | MG | MG- 505 | 2.12 | 0 | Metal Acceptor |
O2B | MG | MG- 505 | 2.44 | 0 | Metal Acceptor |