2.100 Å
X-ray
2001-07-27
Name: | Deoxyribodipyrimidine photo-lyase |
---|---|
ID: | PHR_THET8 |
AC: | P61497 |
Organism: | Thermus thermophilus |
Reign: | Bacteria |
TaxID: | 300852 |
EC Number: | 4.1.99.3 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 37.253 |
---|---|
Number of residues: | 48 |
Including | |
Standard Amino Acids: | 48 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.376 | 2129.625 |
% Hydrophobic | % Polar |
---|---|
41.84 | 58.16 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 78.38 % |
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 |
---|---|---|
30.4713 | 17.4308 | 41.3883 |
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 |
O2A | OH | TYR- 197 | 2.65 | 149.56 | H-Bond (Protein Donor) |
O1A | OG | SER- 210 | 2.65 | 165.74 | H-Bond (Protein Donor) |
O1A | N | SER- 210 | 2.84 | 162.03 | H-Bond (Protein Donor) |
O2P | N | ARG- 211 | 2.58 | 152.62 | H-Bond (Protein Donor) |
O1P | N | LEU- 212 | 3.02 | 123.36 | H-Bond (Protein Donor) |
C3B | CB | SER- 213 | 4.45 | 0 | Hydrophobic |
C5' | CB | SER- 213 | 3.56 | 0 | Hydrophobic |
O1P | N | SER- 213 | 3.11 | 144.13 | H-Bond (Protein Donor) |
C4B | CE1 | PHE- 216 | 4.21 | 0 | Hydrophobic |
C3B | CD1 | PHE- 216 | 4.34 | 0 | Hydrophobic |
O1A | NE1 | TRP- 241 | 3.01 | 158.41 | H-Bond (Protein Donor) |
C5B | CE2 | TRP- 241 | 3.77 | 0 | Hydrophobic |
C1B | CB | GLU- 244 | 4.45 | 0 | Hydrophobic |
C4B | CD2 | LEU- 245 | 3.76 | 0 | Hydrophobic |
O2B | NH1 | ARG- 248 | 2.88 | 130.73 | H-Bond (Protein Donor) |
O2 | NH2 | ARG- 248 | 3.44 | 128.5 | H-Bond (Protein Donor) |
O2 | NH1 | ARG- 248 | 2.79 | 156.03 | H-Bond (Protein Donor) |
C1B | CB | ARG- 248 | 4.43 | 0 | Hydrophobic |
C5' | CZ | PHE- 307 | 4.11 | 0 | Hydrophobic |
C2' | CB | ASN- 310 | 4.35 | 0 | Hydrophobic |
C4' | CB | ASN- 310 | 4.45 | 0 | Hydrophobic |
O2' | OD1 | ASN- 310 | 2.73 | 165.44 | H-Bond (Ligand Donor) |
C6 | CD | ARG- 313 | 4.23 | 0 | Hydrophobic |
C2' | CD | ARG- 313 | 4.5 | 0 | Hydrophobic |
C9A | CD | ARG- 313 | 3.76 | 0 | Hydrophobic |
C8 | CB | ARG- 313 | 3.8 | 0 | Hydrophobic |
C8M | CB | MET- 314 | 3.97 | 0 | Hydrophobic |
C7M | CB | ALA- 317 | 3.63 | 0 | Hydrophobic |
C7M | CE2 | PHE- 335 | 4.45 | 0 | Hydrophobic |
N3 | O | ASP- 341 | 2.74 | 152.43 | H-Bond (Ligand Donor) |
O4 | N | ASP- 343 | 3.11 | 161.02 | H-Bond (Protein Donor) |
C1' | CG1 | VAL- 346 | 4.13 | 0 | Hydrophobic |
N5 | ND2 | ASN- 347 | 2.98 | 170.82 | H-Bond (Protein Donor) |
C7M | CE2 | TRP- 351 | 4.4 | 0 | Hydrophobic |