1.900 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: | 15.588 |
---|---|
Number of residues: | 38 |
Including | |
Standard Amino Acids: | 35 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 2 |
Cofactors: | |
Metals: | CA |
Ligandability | Volume (Å3) |
---|---|
0.768 | 1373.625 |
% Hydrophobic | % Polar |
---|---|
34.89 | 65.11 |
According to VolSite |
HET Code: | ATP |
---|---|
Formula: | C10H12N5O13P3 |
Molecular weight: | 503.149 g/mol |
DrugBank ID: | DB00171 |
Buried Surface Area: | 67.76 % |
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 |
---|---|---|
19.5504 | -7.18274 | 12.6281 |
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 | 2.55 | 141.58 | H-Bond (Protein Donor) |
O3G | OG | SER- 153 | 2.78 | 158.26 | H-Bond (Protein Donor) |
N7 | N | GLY- 270 | 3.19 | 139.11 | H-Bond (Protein Donor) |
N6 | OD1 | ASN- 292 | 3.48 | 129.82 | H-Bond (Ligand Donor) |
N6 | O | THR- 293 | 2.68 | 150.09 | H-Bond (Ligand Donor) |
C2' | CE1 | TYR- 294 | 3.74 | 0 | Hydrophobic |
C5' | CB | PRO- 296 | 4.44 | 0 | Hydrophobic |
O2A | OG1 | THR- 297 | 2.86 | 152.02 | H-Bond (Protein Donor) |
O2A | N | THR- 297 | 3.04 | 153.07 | H-Bond (Protein Donor) |
O3' | OD1 | ASP- 383 | 2.55 | 157.57 | H-Bond (Ligand Donor) |
O3' | OD2 | ASP- 383 | 3.31 | 141.24 | H-Bond (Ligand Donor) |
O2' | OD1 | ASP- 383 | 3.36 | 131.66 | H-Bond (Ligand Donor) |
O2' | OD2 | ASP- 383 | 2.83 | 167.8 | H-Bond (Ligand Donor) |
O2' | OH | TYR- 394 | 2.78 | 134.89 | H-Bond (Protein Donor) |
C2' | CE1 | TYR- 394 | 3.66 | 0 | Hydrophobic |
O1B | NH2 | ARG- 397 | 2.82 | 156.69 | H-Bond (Protein Donor) |
O2B | NH1 | ARG- 397 | 3.09 | 170.71 | H-Bond (Protein Donor) |
O1B | CZ | ARG- 397 | 3.72 | 0 | Ionic (Protein Cationic) |
O2B | CZ | ARG- 397 | 3.84 | 0 | Ionic (Protein Cationic) |
O1B | NZ | LYS- 492 | 2.63 | 0 | Ionic (Protein Cationic) |
O1A | NZ | LYS- 492 | 3.97 | 0 | Ionic (Protein Cationic) |
O1G | CA | CA- 710 | 2.57 | 0 | Metal Acceptor |
O2B | CA | CA- 710 | 2.39 | 0 | Metal Acceptor |
N1 | O | HOH- 806 | 2.89 | 176.19 | H-Bond (Protein Donor) |
O5' | O | HOH- 863 | 2.82 | 171.39 | H-Bond (Protein Donor) |