2.000 Å
X-ray
2006-10-02
Name: | Poly(A) polymerase, putative |
---|---|
ID: | Q381M1_TRYB2 |
AC: | Q381M1 |
Organism: | Trypanosoma brucei brucei |
Reign: | Eukaryota |
TaxID: | 185431 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 22.823 |
---|---|
Number of residues: | 41 |
Including | |
Standard Amino Acids: | 36 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 4 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.487 | 1053.000 |
% Hydrophobic | % Polar |
---|---|
35.90 | 64.10 |
According to VolSite |
HET Code: | UTP |
---|---|
Formula: | C9H11N2O15P3 |
Molecular weight: | 480.109 g/mol |
DrugBank ID: | DB04005 |
Buried Surface Area: | 60.74 % |
Polar Surface area: | 299.67 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 15 |
H-Bond Donors: | 3 |
Rings: | 2 |
Aromatic rings: | 0 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
23.8611 | 22.2748 | -46.7755 |
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 |
C1' | CE2 | PHE- 52 | 3.78 | 0 | Hydrophobic |
C4' | CE2 | PHE- 52 | 3.58 | 0 | Hydrophobic |
C2' | CD2 | PHE- 52 | 4.26 | 0 | Hydrophobic |
O1B | N | SER- 54 | 2.66 | 160.87 | H-Bond (Protein Donor) |
C5' | CB | ASP- 68 | 4.43 | 0 | Hydrophobic |
O2' | OD1 | ASN- 147 | 2.53 | 168 | H-Bond (Ligand Donor) |
O2 | ND2 | ASN- 147 | 3.05 | 152.34 | H-Bond (Protein Donor) |
O3' | OG | SER- 148 | 2.95 | 136.67 | H-Bond (Ligand Donor) |
O3B | NZ | LYS- 169 | 3.32 | 151.08 | H-Bond (Protein Donor) |
O2G | NZ | LYS- 169 | 2.96 | 141.91 | H-Bond (Protein Donor) |
O2G | NZ | LYS- 169 | 2.96 | 0 | Ionic (Protein Cationic) |
O1G | NZ | LYS- 173 | 2.81 | 167.64 | H-Bond (Protein Donor) |
O1G | NZ | LYS- 173 | 2.81 | 0 | Ionic (Protein Cationic) |
O2G | NZ | LYS- 173 | 3.69 | 0 | Ionic (Protein Cationic) |
O1G | OG | SER- 188 | 2.58 | 155.23 | H-Bond (Protein Donor) |
O2A | N | TYR- 189 | 3.35 | 151.85 | H-Bond (Protein Donor) |
C2' | CD1 | TYR- 189 | 3.91 | 0 | Hydrophobic |
C3' | CB | TYR- 189 | 4.16 | 0 | Hydrophobic |
O1A | MG | MG- 401 | 2.49 | 0 | Metal Acceptor |
O1B | MG | MG- 401 | 2.42 | 0 | Metal Acceptor |
O3G | MG | MG- 401 | 2.24 | 0 | Metal Acceptor |