2.900 Å
X-ray
2002-03-29
Name: | Valine--tRNA ligase |
---|---|
ID: | SYV_THETH |
AC: | P96142 |
Organism: | Thermus thermophilus |
Reign: | Bacteria |
TaxID: | 274 |
EC Number: | 6.1.1.9 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 36.049 |
---|---|
Number of residues: | 38 |
Including | |
Standard Amino Acids: | 38 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.310 | 435.375 |
% Hydrophobic | % Polar |
---|---|
41.86 | 58.14 |
According to VolSite |
HET Code: | VAA |
---|---|
Formula: | C15H25N8O6S |
Molecular weight: | 445.474 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 78.12 % |
Polar Surface area: | 230.59 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 10 |
H-Bond Donors: | 6 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 0 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 7 |
X | Y | Z |
---|---|---|
174.744 | 120.02 | 18.5097 |
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 |
CG1 | CB | PRO- 41 | 3.53 | 0 | Hydrophobic |
C4' | CB | PRO- 41 | 3.99 | 0 | Hydrophobic |
N | O | PRO- 42 | 2.82 | 152.2 | H-Bond (Ligand Donor) |
CG1 | CG | PRO- 42 | 4.15 | 0 | Hydrophobic |
CG2 | CG | PRO- 42 | 4.41 | 0 | Hydrophobic |
N | OD1 | ASN- 44 | 2.6 | 168.73 | H-Bond (Ligand Donor) |
O1S | N | ASN- 44 | 3.48 | 156.77 | H-Bond (Protein Donor) |
O1S | NE2 | HIS- 53 | 3.08 | 142.03 | H-Bond (Protein Donor) |
N | OD2 | ASP- 81 | 3.25 | 153.43 | H-Bond (Ligand Donor) |
N | OD2 | ASP- 81 | 3.25 | 0 | Ionic (Ligand Cationic) |
CG2 | CZ3 | TRP- 456 | 3.71 | 0 | Hydrophobic |
CG2 | CB | SER- 459 | 3.55 | 0 | Hydrophobic |
C3' | CB | THR- 487 | 4.43 | 0 | Hydrophobic |
O3' | OG1 | THR- 487 | 2.73 | 164.51 | H-Bond (Protein Donor) |
O2' | N | GLY- 488 | 2.74 | 133.14 | H-Bond (Protein Donor) |
O3' | N | GLY- 488 | 3.49 | 154.16 | H-Bond (Protein Donor) |
O2' | OD1 | ASP- 490 | 2.7 | 173.03 | H-Bond (Ligand Donor) |
CB | CD1 | ILE- 491 | 3.77 | 0 | Hydrophobic |
C3' | CD1 | ILE- 491 | 3.63 | 0 | Hydrophobic |
CG2 | CE2 | TRP- 495 | 3.64 | 0 | Hydrophobic |
CB | CD2 | TRP- 495 | 4.18 | 0 | Hydrophobic |
N3 | NE2 | HIS- 518 | 3.38 | 151.77 | H-Bond (Protein Donor) |
N1 | N | VAL- 521 | 2.96 | 157.17 | H-Bond (Protein Donor) |
N6 | O | VAL- 521 | 3.25 | 169.58 | H-Bond (Ligand Donor) |
N6 | O | MET- 529 | 2.8 | 152.79 | H-Bond (Ligand Donor) |