2.250 Å
X-ray
2002-01-03
Name: | Flavin-dependent thymidylate synthase |
---|---|
ID: | THYX_THEMA |
AC: | Q9WYT0 |
Organism: | Thermotoga maritima |
Reign: | Bacteria |
TaxID: | 243274 |
EC Number: | 2.1.1.148 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 41 % |
C | 29 % |
D | 29 % |
B-Factor: | 26.726 |
---|---|
Number of residues: | 43 |
Including | |
Standard Amino Acids: | 40 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 2 |
Cofactors: | FAD |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.257 | 2497.500 |
% Hydrophobic | % Polar |
---|---|
34.32 | 65.68 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 58.17 % |
Polar Surface area: | 381.7 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 22 |
H-Bond Donors: | 7 |
Rings: | 6 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 13 |
X | Y | Z |
---|---|---|
42.9097 | 36.2923 | 109.41 |
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 |
C4' | CG2 | THR- 55 | 4.01 | 0 | Hydrophobic |
N1 | NH1 | ARG- 78 | 3.28 | 133.56 | H-Bond (Protein Donor) |
O2 | NH1 | ARG- 78 | 3.12 | 161.67 | H-Bond (Protein Donor) |
C5' | CB | ARG- 78 | 4.19 | 0 | Hydrophobic |
O2A | N | ARG- 80 | 2.89 | 153.81 | H-Bond (Protein Donor) |
O2A | NE | ARG- 80 | 2.97 | 155.95 | H-Bond (Protein Donor) |
O2A | NH2 | ARG- 80 | 3.37 | 135.19 | H-Bond (Protein Donor) |
O1P | NH2 | ARG- 80 | 3.31 | 142.12 | H-Bond (Protein Donor) |
O2A | CZ | ARG- 80 | 3.61 | 0 | Ionic (Protein Cationic) |
O1A | N | ILE- 81 | 3.22 | 172.68 | H-Bond (Protein Donor) |
C5B | CG1 | ILE- 81 | 3.54 | 0 | Hydrophobic |
O2 | N | GLU- 86 | 2.81 | 151.71 | H-Bond (Protein Donor) |
N3 | O | GLU- 86 | 2.9 | 136.91 | H-Bond (Ligand Donor) |
N1A | ND2 | ASN- 163 | 2.6 | 164.75 | H-Bond (Protein Donor) |
C2B | CD | ARG- 165 | 4.2 | 0 | Hydrophobic |
O1P | NH2 | ARG- 165 | 2.67 | 137.05 | H-Bond (Protein Donor) |
O1P | CZ | ARG- 165 | 3.67 | 0 | Ionic (Protein Cationic) |
O2P | ND2 | ASN- 169 | 2.74 | 171.47 | H-Bond (Protein Donor) |
C8M | CB | LEU- 173 | 4.34 | 0 | Hydrophobic |
C8M | CD | ARG- 174 | 4.31 | 0 | Hydrophobic |
C7M | CB | HIS- 178 | 3.74 | 0 | Hydrophobic |
C8M | CB | ALA- 179 | 4.33 | 0 | Hydrophobic |
C4B | C1B | FAD- 300 | 4.12 | 0 | Hydrophobic |
C2B | C4B | FAD- 300 | 4.11 | 0 | Hydrophobic |
O1A | O | HOH- 337 | 2.87 | 179.96 | H-Bond (Protein Donor) |