2.610 Å
X-ray
2016-06-03
Name: | Riboflavin transporter RibU |
---|---|
ID: | RIBU_THEMA |
AC: | Q9X1G6 |
Organism: | Thermotoga maritima |
Reign: | Bacteria |
TaxID: | 243274 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 57.746 |
---|---|
Number of residues: | 33 |
Including | |
Standard Amino Acids: | 33 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.526 | 388.125 |
% Hydrophobic | % Polar |
---|---|
47.83 | 52.17 |
According to VolSite |
HET Code: | RBF |
---|---|
Formula: | C17H20N4O6 |
Molecular weight: | 376.364 g/mol |
DrugBank ID: | DB00140 |
Buried Surface Area: | 72.66 % |
Polar Surface area: | 155.04 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 9 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 0 |
Cationic atoms: | 0 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 5 |
X | Y | Z |
---|---|---|
-25.7275 | 0.0701852 | 83.1169 |
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 |
O4' | OE1 | GLU- 24 | 3.31 | 150.68 | H-Bond (Ligand Donor) |
C8M | CB | PHE- 33 | 4.48 | 0 | Hydrophobic |
C7 | CD1 | PHE- 33 | 3.41 | 0 | Hydrophobic |
C6 | CD2 | LEU- 34 | 4.23 | 0 | Hydrophobic |
C9A | CD2 | LEU- 34 | 4 | 0 | Hydrophobic |
O2' | N | LYS- 35 | 2.66 | 159.34 | H-Bond (Protein Donor) |
O5' | NZ | LYS- 35 | 3.36 | 144.48 | H-Bond (Protein Donor) |
C4' | CG | LYS- 35 | 3.89 | 0 | Hydrophobic |
C8M | CG1 | VAL- 75 | 4.21 | 0 | Hydrophobic |
C6 | CE | MET- 79 | 4.37 | 0 | Hydrophobic |
C9A | CB | MET- 79 | 4.07 | 0 | Hydrophobic |
C1' | CB | ASN- 80 | 4.31 | 0 | Hydrophobic |
O4 | ND2 | ASN- 123 | 2.79 | 157.13 | H-Bond (Protein Donor) |
C7M | CG2 | ILE- 126 | 3.96 | 0 | Hydrophobic |
C6 | CG2 | VAL- 127 | 4.37 | 0 | Hydrophobic |
C7M | CG2 | VAL- 127 | 3.72 | 0 | Hydrophobic |
C7M | CD2 | TYR- 130 | 4.1 | 0 | Hydrophobic |
C8M | CZ | TYR- 130 | 3.86 | 0 | Hydrophobic |
N3 | OD1 | ASN- 149 | 2.71 | 168.85 | H-Bond (Ligand Donor) |
O4 | ND2 | ASN- 149 | 2.9 | 172.79 | H-Bond (Protein Donor) |
O2 | NZ | LYS- 152 | 2.6 | 151.28 | H-Bond (Protein Donor) |