2.840 Å
X-ray
2012-02-13
Name: | Lysine--tRNA ligase |
---|---|
ID: | SYK_HUMAN |
AC: | Q15046 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 6.1.1.6 |
Chain Name: | Percentage of Residues within binding site |
---|---|
H | 100 % |
B-Factor: | 33.407 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 33 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 0 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.797 | 1535.625 |
% Hydrophobic | % Polar |
---|---|
34.51 | 65.49 |
According to VolSite |
HET Code: | APC |
---|---|
Formula: | C11H14N5O12P3 |
Molecular weight: | 501.176 g/mol |
DrugBank ID: | DB02596 |
Buried Surface Area: | 48.53 % |
Polar Surface area: | 310.64 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 16 |
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 |
---|---|---|
52.1686 | -10.7191 | 27.6535 |
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 |
O1B | NE2 | HIS- 331 | 3.29 | 140.75 | H-Bond (Protein Donor) |
N1 | N | ASN- 332 | 3.41 | 163.19 | H-Bond (Protein Donor) |
C1' | CE2 | PHE- 335 | 4.14 | 0 | Hydrophobic |
DuAr | DuAr | PHE- 335 | 3.89 | 0 | Aromatic Face/Face |
O2B | NH2 | ARG- 553 | 2.97 | 144.13 | H-Bond (Protein Donor) |
O2B | CZ | ARG- 553 | 3.89 | 0 | Ionic (Protein Cationic) |
O1A | MG | MG- 604 | 2.17 | 0 | Metal Acceptor |