2.060 Å
X-ray
2000-01-28
Name: | NH(3)-dependent NAD(+) synthetase |
---|---|
ID: | NADE_BACSU |
AC: | P08164 |
Organism: | Bacillus subtilis |
Reign: | Bacteria |
TaxID: | 224308 |
EC Number: | 6.3.1.5 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 67 % |
B | 33 % |
B-Factor: | 19.952 |
---|---|
Number of residues: | 48 |
Including | |
Standard Amino Acids: | 44 |
Non Standard Amino Acids: | 2 |
Water Molecules: | 2 |
Cofactors: | ATP |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.072 | 445.500 |
% Hydrophobic | % Polar |
---|---|
46.97 | 53.03 |
According to VolSite |
HET Code: | DND |
---|---|
Formula: | C21H24N6O15P2 |
Molecular weight: | 662.394 g/mol |
DrugBank ID: | DB04099 |
Buried Surface Area: | 63.91 % |
Polar Surface area: | 340.58 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 19 |
H-Bond Donors: | 5 |
Rings: | 5 |
Aromatic rings: | 3 |
Anionic atoms: | 3 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 11 |
X | Y | Z |
---|---|---|
17.8064 | 56.8204 | 34.9889 |
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 |
N1A | OH | TYR- 32 | 2.64 | 164.5 | H-Bond (Protein Donor) |
C3D | CE1 | PHE- 129 | 3.81 | 0 | Hydrophobic |
C5D | CZ | PHE- 129 | 4.3 | 0 | Hydrophobic |
C5N | CB | ALA- 136 | 4.36 | 0 | Hydrophobic |
O13 | NH2 | ARG- 137 | 2.73 | 143.52 | H-Bond (Protein Donor) |
O13 | CZ | ARG- 137 | 3.75 | 0 | Ionic (Protein Cationic) |
C2B | CE2 | TYR- 144 | 4.27 | 0 | Hydrophobic |
C2B | CD2 | LEU- 153 | 4.15 | 0 | Hydrophobic |
C2D | CE1 | PHE- 167 | 4.03 | 0 | Hydrophobic |
C5D | CB | THR- 169 | 4.43 | 0 | Hydrophobic |
C5N | CB | THR- 169 | 3.95 | 0 | Hydrophobic |
O14 | N | LYS- 170 | 2.72 | 168.56 | H-Bond (Protein Donor) |
O2B | OD2 | ASP- 177 | 2.64 | 158.29 | H-Bond (Ligand Donor) |
C3N | CB | ALA- 209 | 3.5 | 0 | Hydrophobic |
C5N | CD1 | LEU- 211 | 3.4 | 0 | Hydrophobic |
O2D | OE2 | GLU- 223 | 3.2 | 154.93 | H-Bond (Ligand Donor) |
DuAr | DuAr | HIS- 257 | 3.52 | 0 | Aromatic Face/Face |
O12 | NZ | LYS- 258 | 2.69 | 163.63 | H-Bond (Protein Donor) |
O12 | NZ | LYS- 258 | 2.69 | 0 | Ionic (Protein Cationic) |
O14 | NZ | LYS- 258 | 3.13 | 0 | Ionic (Protein Cationic) |
C4N | C5' | ATP- 5000 | 4.5 | 0 | Hydrophobic |