1.600 Å
X-ray
2001-02-07
Name: | UDP-sulfoquinovose synthase, chloroplastic |
---|---|
ID: | SQD1_ARATH |
AC: | O48917 |
Organism: | Arabidopsis thaliana |
Reign: | Eukaryota |
TaxID: | 3702 |
EC Number: | 3.13.1.1 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 14.023 |
---|---|
Number of residues: | 57 |
Including | |
Standard Amino Acids: | 49 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 7 |
Cofactors: | NAD |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.996 | 766.125 |
% Hydrophobic | % Polar |
---|---|
46.26 | 53.74 |
According to VolSite |
HET Code: | UPG |
---|---|
Formula: | C15H22N2O17P2 |
Molecular weight: | 564.286 g/mol |
DrugBank ID: | DB01861 |
Buried Surface Area: | 80.89 % |
Polar Surface area: | 316.82 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 7 |
Rings: | 3 |
Aromatic rings: | 0 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 9 |
X | Y | Z |
---|---|---|
70.8445 | 98.2715 | 26.1238 |
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 |
O2' | O | ARG- 101 | 3.25 | 161.65 | H-Bond (Ligand Donor) |
O3' | O | ARG- 101 | 2.73 | 168.55 | H-Bond (Ligand Donor) |
O2' | NH2 | ARG- 101 | 2.98 | 136.04 | H-Bond (Protein Donor) |
C2' | CD | ARG- 101 | 4.07 | 0 | Hydrophobic |
C6' | CB | ALA- 145 | 4.49 | 0 | Hydrophobic |
O6' | N | GLY- 147 | 3.16 | 136.49 | H-Bond (Protein Donor) |
O4' | OH | TYR- 182 | 2.61 | 160.29 | H-Bond (Protein Donor) |
C3' | CE2 | TYR- 182 | 3.55 | 0 | Hydrophobic |
C5C | CG2 | VAL- 211 | 4.46 | 0 | Hydrophobic |
C1' | CG2 | VAL- 211 | 4.4 | 0 | Hydrophobic |
C1' | CG2 | THR- 238 | 3.9 | 0 | Hydrophobic |
O2A | N | ALA- 239 | 2.73 | 174.18 | H-Bond (Protein Donor) |
O4 | NE | ARG- 242 | 2.84 | 160 | H-Bond (Protein Donor) |
O4 | NH2 | ARG- 242 | 3.16 | 137.42 | H-Bond (Protein Donor) |
N3 | O | THR- 254 | 2.81 | 166.13 | H-Bond (Ligand Donor) |
O4 | OG1 | THR- 254 | 2.86 | 138.8 | H-Bond (Protein Donor) |
O2 | N | TYR- 256 | 3 | 159.31 | H-Bond (Protein Donor) |
C2C | CD2 | TYR- 256 | 4 | 0 | Hydrophobic |
C4C | CG | ARG- 263 | 4.35 | 0 | Hydrophobic |
C1C | CG2 | VAL- 300 | 3.9 | 0 | Hydrophobic |
C4C | CG2 | VAL- 300 | 4.44 | 0 | Hydrophobic |
C2C | CD | ARG- 327 | 4.21 | 0 | Hydrophobic |
O1A | NH1 | ARG- 327 | 2.82 | 130.1 | H-Bond (Protein Donor) |
O1B | NH2 | ARG- 327 | 2.83 | 152.49 | H-Bond (Protein Donor) |
O1B | NH1 | ARG- 327 | 3.33 | 130.83 | H-Bond (Protein Donor) |
O1A | CZ | ARG- 327 | 3.64 | 0 | Ionic (Protein Cationic) |
O1B | CZ | ARG- 327 | 3.5 | 0 | Ionic (Protein Cationic) |
O2C | OE2 | GLU- 329 | 2.66 | 142.22 | H-Bond (Ligand Donor) |
O3C | OE1 | GLU- 329 | 2.71 | 170.33 | H-Bond (Ligand Donor) |
C2' | C3N | NAD- 401 | 4.02 | 0 | Hydrophobic |
C3' | C4N | NAD- 401 | 4.25 | 0 | Hydrophobic |
C4' | C5N | NAD- 401 | 3.36 | 0 | Hydrophobic |
C5' | C4N | NAD- 401 | 4.05 | 0 | Hydrophobic |
C6' | C5N | NAD- 401 | 3.84 | 0 | Hydrophobic |
O3' | O2D | NAD- 401 | 2.85 | 172.04 | H-Bond (Protein Donor) |
O2B | O | HOH- 460 | 2.7 | 179.96 | H-Bond (Protein Donor) |