2.320 Å
X-ray
2008-11-21
Name: | D-alanine--poly(phosphoribitol) ligase subunit 1 |
---|---|
ID: | DLTA_BACCR |
AC: | Q81G39 |
Organism: | Bacillus cereus |
Reign: | Bacteria |
TaxID: | 226900 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 34.668 |
---|---|
Number of residues: | 39 |
Including | |
Standard Amino Acids: | 35 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 3 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.417 | 1984.500 |
% Hydrophobic | % Polar |
---|---|
37.93 | 62.07 |
According to VolSite |
HET Code: | ATP |
---|---|
Formula: | C10H12N5O13P3 |
Molecular weight: | 503.149 g/mol |
DrugBank ID: | DB00171 |
Buried Surface Area: | 64.17 % |
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 |
---|---|---|
19.1245 | -7.1881 | 13.4554 |
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 |
O3G | OG1 | THR- 152 | 2.67 | 148.29 | H-Bond (Protein Donor) |
O2G | OG | SER- 153 | 2.76 | 129.67 | H-Bond (Protein Donor) |
O3G | N | SER- 153 | 2.85 | 155.65 | H-Bond (Protein Donor) |
O3G | OG | SER- 153 | 2.87 | 152.79 | H-Bond (Protein Donor) |
N7 | N | GLY- 270 | 3.33 | 126.13 | H-Bond (Protein Donor) |
N6 | OD1 | ASN- 292 | 3.38 | 131.2 | H-Bond (Ligand Donor) |
N6 | O | THR- 293 | 2.78 | 154.79 | H-Bond (Ligand Donor) |
C2' | CE1 | TYR- 294 | 3.73 | 0 | Hydrophobic |
O2A | OG1 | THR- 297 | 2.67 | 171.41 | H-Bond (Protein Donor) |
O2A | N | THR- 297 | 2.95 | 127.83 | H-Bond (Protein Donor) |
O3' | OD1 | ASP- 383 | 2.61 | 160.87 | H-Bond (Ligand Donor) |
C2' | CE1 | TYR- 394 | 3.72 | 0 | Hydrophobic |
C1' | CZ | TYR- 394 | 4.5 | 0 | Hydrophobic |
O2' | OH | TYR- 394 | 2.65 | 150.19 | H-Bond (Ligand Donor) |
O1B | NH2 | ARG- 397 | 2.99 | 156.93 | H-Bond (Protein Donor) |
O2B | NH2 | ARG- 397 | 3.31 | 130.6 | H-Bond (Protein Donor) |
O2B | NH1 | ARG- 397 | 2.69 | 168.47 | H-Bond (Protein Donor) |
O1B | CZ | ARG- 397 | 3.91 | 0 | Ionic (Protein Cationic) |
O2B | CZ | ARG- 397 | 3.44 | 0 | Ionic (Protein Cationic) |
O1B | NZ | LYS- 492 | 3.17 | 164.27 | H-Bond (Protein Donor) |
O1B | NZ | LYS- 492 | 3.17 | 0 | Ionic (Protein Cationic) |
O1G | MG | MG- 710 | 2.48 | 0 | Metal Acceptor |
N1 | O | HOH- 806 | 2.62 | 176.18 | H-Bond (Protein Donor) |
O5' | O | HOH- 895 | 2.62 | 165.79 | H-Bond (Protein Donor) |