2.800 Å
X-ray
2006-10-10
Name: | DNA photolyase |
---|---|
ID: | F9VNB1_SULTO |
AC: | F9VNB1 |
Organism: | Sulfolobus tokodaii |
Reign: | Archaea |
TaxID: | 273063 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 21.290 |
---|---|
Number of residues: | 48 |
Including | |
Standard Amino Acids: | 47 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.599 | 907.875 |
% Hydrophobic | % Polar |
---|---|
48.70 | 51.30 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 66.98 % |
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 |
---|---|---|
13.7646 | 26.5745 | -4.24691 |
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 |
C3' | CB | ARG- 8 | 4.38 | 0 | Hydrophobic |
C2' | CD | ARG- 9 | 4.24 | 0 | Hydrophobic |
C3' | CB | ARG- 9 | 4.23 | 0 | Hydrophobic |
C4' | CD | ARG- 9 | 4.35 | 0 | Hydrophobic |
N3 | O | ILE- 34 | 2.71 | 168.89 | H-Bond (Ligand Donor) |
O4 | N | ASP- 36 | 3 | 166.52 | H-Bond (Protein Donor) |
O2A | NE2 | GLN- 39 | 2.72 | 161.23 | H-Bond (Protein Donor) |
O3' | NE2 | GLN- 39 | 3.23 | 174.54 | H-Bond (Protein Donor) |
C5B | CG | GLN- 39 | 3.7 | 0 | Hydrophobic |
C6 | CB | GLN- 39 | 4.03 | 0 | Hydrophobic |
C6 | CD2 | LEU- 40 | 4.02 | 0 | Hydrophobic |
O2B | OD1 | ASN- 43 | 2.58 | 162.04 | H-Bond (Ligand Donor) |
C2B | CB | TYR- 45 | 4.15 | 0 | Hydrophobic |
DuAr | DuAr | TYR- 45 | 3.47 | 0 | Aromatic Face/Face |
C7M | CG | LYS- 46 | 3.77 | 0 | Hydrophobic |
C8M | CB | ALA- 50 | 4.22 | 0 | Hydrophobic |
C7M | CG2 | VAL- 51 | 3.57 | 0 | Hydrophobic |
C1' | SD | MET- 54 | 4.32 | 0 | Hydrophobic |
C9A | SD | MET- 54 | 3.67 | 0 | Hydrophobic |
O4' | OD2 | ASP- 98 | 2.82 | 167.69 | H-Bond (Ligand Donor) |
O1P | OG1 | THR- 100 | 2.53 | 162.81 | H-Bond (Protein Donor) |
C5B | CG | PHE- 102 | 3.94 | 0 | Hydrophobic |
C4B | CD2 | PHE- 102 | 3.79 | 0 | Hydrophobic |
C5' | CD1 | PHE- 102 | 3.88 | 0 | Hydrophobic |
O3' | NH1 | ARG- 106 | 3.36 | 142.06 | H-Bond (Protein Donor) |
O4' | NH2 | ARG- 106 | 3.18 | 142.31 | H-Bond (Protein Donor) |
O2' | NZ | LYS- 221 | 3.03 | 147.9 | H-Bond (Protein Donor) |
C8M | CZ | PHE- 222 | 3.92 | 0 | Hydrophobic |
C1' | CE1 | PHE- 222 | 4.27 | 0 | Hydrophobic |
N6A | OE1 | GLU- 331 | 3 | 149.19 | H-Bond (Ligand Donor) |
N7A | OH | TYR- 341 | 2.61 | 162.33 | H-Bond (Protein Donor) |
N6A | OH | TYR- 341 | 2.95 | 152.17 | H-Bond (Ligand Donor) |
C8M | CD1 | TYR- 341 | 4.23 | 0 | Hydrophobic |
O2 | O | HOH- 5040 | 2.75 | 154.54 | H-Bond (Protein Donor) |