1.800 Å
X-ray
2007-01-25
Name: | Adenylate kinase |
---|---|
ID: | KAD_BACSU |
AC: | P16304 |
Organism: | Bacillus subtilis |
Reign: | Bacteria |
TaxID: | 224308 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 12.945 |
---|---|
Number of residues: | 63 |
Including | |
Standard Amino Acids: | 60 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 2 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.051 | 469.125 |
% Hydrophobic | % Polar |
---|---|
46.76 | 53.24 |
According to VolSite |
HET Code: | AP5 |
---|---|
Formula: | C20H24N10O22P5 |
Molecular weight: | 911.327 g/mol |
DrugBank ID: | DB01717 |
Buried Surface Area: | 78.76 % |
Polar Surface area: | 543.69 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 30 |
H-Bond Donors: | 6 |
Rings: | 6 |
Aromatic rings: | 4 |
Anionic atoms: | 5 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 16 |
X | Y | Z |
---|---|---|
37.3449 | 60.7501 | 44.4826 |
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 | GLY- 10 | 3.35 | 136.78 | H-Bond (Protein Donor) |
O1B | N | GLY- 12 | 3.04 | 151.01 | H-Bond (Protein Donor) |
O1B | N | LYS- 13 | 2.87 | 151.37 | H-Bond (Protein Donor) |
O1D | NZ | LYS- 13 | 3.03 | 173.88 | H-Bond (Protein Donor) |
O1D | NZ | LYS- 13 | 3.03 | 0 | Ionic (Protein Cationic) |
O2B | N | GLY- 14 | 2.77 | 157.79 | H-Bond (Protein Donor) |
O1A | N | THR- 15 | 2.82 | 144.53 | H-Bond (Protein Donor) |
O1A | OG1 | THR- 15 | 2.7 | 163.51 | H-Bond (Protein Donor) |
N7B | OG1 | THR- 31 | 2.84 | 167.91 | H-Bond (Protein Donor) |
C1J | CD1 | PHE- 35 | 4.03 | 0 | Hydrophobic |
O1E | CZ | ARG- 36 | 3.65 | 0 | Ionic (Protein Cationic) |
O1E | NH1 | ARG- 36 | 3.1 | 151.09 | H-Bond (Protein Donor) |
O1E | NH2 | ARG- 36 | 3.33 | 139.76 | H-Bond (Protein Donor) |
C4J | CG1 | ILE- 53 | 4.08 | 0 | Hydrophobic |
C1J | CG1 | ILE- 53 | 3.87 | 0 | Hydrophobic |
O2J | O | GLU- 57 | 2.61 | 155.79 | H-Bond (Ligand Donor) |
C1J | CG2 | VAL- 59 | 4.23 | 0 | Hydrophobic |
N3B | N | VAL- 59 | 3.05 | 152.42 | H-Bond (Protein Donor) |
N6B | O | GLY- 85 | 2.9 | 131.84 | H-Bond (Ligand Donor) |
O1D | NH2 | ARG- 88 | 3.12 | 142.13 | H-Bond (Protein Donor) |
O1D | NH1 | ARG- 88 | 2.93 | 153.43 | H-Bond (Protein Donor) |
O2E | NH2 | ARG- 88 | 2.96 | 125.66 | H-Bond (Protein Donor) |
N7B | NE | ARG- 88 | 3.31 | 120.73 | H-Bond (Protein Donor) |
O1D | CZ | ARG- 88 | 3.47 | 0 | Ionic (Protein Cationic) |
N6B | OE1 | GLN- 92 | 2.91 | 173.83 | H-Bond (Ligand Donor) |
N1B | NE2 | GLN- 92 | 3.04 | 157.69 | H-Bond (Protein Donor) |
C4F | CB | ARG- 123 | 4.31 | 0 | Hydrophobic |
DuAr | CZ | ARG- 123 | 3.64 | 7.65 | Pi/Cation |
C5F | CD2 | LEU- 124 | 4.33 | 0 | Hydrophobic |
O2A | CZ | ARG- 127 | 3.93 | 0 | Ionic (Protein Cationic) |
O1G | CZ | ARG- 127 | 3.38 | 0 | Ionic (Protein Cationic) |
O2G | CZ | ARG- 127 | 3.8 | 0 | Ionic (Protein Cationic) |
O2A | NH2 | ARG- 127 | 2.86 | 142.25 | H-Bond (Protein Donor) |
O1G | NH1 | ARG- 127 | 2.87 | 123.16 | H-Bond (Protein Donor) |
O2G | NH2 | ARG- 127 | 2.94 | 170.39 | H-Bond (Protein Donor) |
C3F | CD | ARG- 127 | 3.69 | 0 | Hydrophobic |
O2A | OG1 | THR- 136 | 3.42 | 153.78 | H-Bond (Protein Donor) |
C3F | CB | THR- 136 | 4.17 | 0 | Hydrophobic |
O3F | O | TYR- 137 | 2.73 | 152.34 | H-Bond (Ligand Donor) |
C1F | CB | HIS- 138 | 4.28 | 0 | Hydrophobic |
O1G | CZ | ARG- 160 | 3.82 | 0 | Ionic (Protein Cationic) |
O2G | CZ | ARG- 160 | 3.98 | 0 | Ionic (Protein Cationic) |
O1E | CZ | ARG- 160 | 3.64 | 0 | Ionic (Protein Cationic) |
O2G | NH2 | ARG- 160 | 3.09 | 143.53 | H-Bond (Protein Donor) |
O1E | NH2 | ARG- 160 | 3.14 | 123.07 | H-Bond (Protein Donor) |
O2D | CZ | ARG- 171 | 3.78 | 0 | Ionic (Protein Cationic) |
O2D | NH1 | ARG- 171 | 2.84 | 162.58 | H-Bond (Protein Donor) |
N6A | O | ARG- 199 | 2.85 | 175.12 | H-Bond (Ligand Donor) |
O2B | MG | MG- 923 | 2.51 | 0 | Metal Acceptor |
O2G | MG | MG- 923 | 2.55 | 0 | Metal Acceptor |
O3J | O | HOH- 1228 | 2.79 | 179.96 | H-Bond (Protein Donor) |