2.700 Å
X-ray
2011-06-15
Name: | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC |
---|---|
ID: | MNMC_YERPE |
AC: | Q8ZD36 |
Organism: | Yersinia pestis |
Reign: | Bacteria |
TaxID: | 632 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 21.614 |
---|---|
Number of residues: | 70 |
Including | |
Standard Amino Acids: | 64 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 5 |
Cofactors: | |
Metals: | CL |
Ligandability | Volume (Å3) |
---|---|
0.968 | 1586.250 |
% Hydrophobic | % Polar |
---|---|
41.49 | 58.51 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 72.79 % |
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 |
---|---|---|
8.16874 | 4.45153 | 0.488472 |
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 |
C4' | CG2 | ILE- 274 | 4.3 | 0 | Hydrophobic |
O1P | N | VAL- 275 | 3.22 | 161.74 | H-Bond (Protein Donor) |
N3A | N | ALA- 295 | 2.92 | 139.19 | H-Bond (Protein Donor) |
O1A | N | ALA- 303 | 2.65 | 158.11 | H-Bond (Protein Donor) |
O2A | N | ALA- 303 | 3.45 | 123.51 | H-Bond (Protein Donor) |
C8M | CB | ALA- 303 | 4.2 | 0 | Hydrophobic |
C3' | CB | ALA- 303 | 4.42 | 0 | Hydrophobic |
O2A | OG | SER- 304 | 2.56 | 159.66 | H-Bond (Protein Donor) |
O4' | OG | SER- 304 | 3.24 | 148.22 | H-Bond (Ligand Donor) |
N3 | O | ALA- 310 | 2.78 | 161.59 | H-Bond (Ligand Donor) |
O4 | N | ALA- 310 | 2.99 | 147.9 | H-Bond (Protein Donor) |
N6A | O | LEU- 435 | 3.46 | 154.87 | H-Bond (Ligand Donor) |
N1A | N | LEU- 435 | 2.88 | 157.87 | H-Bond (Protein Donor) |
C1B | CG2 | THR- 465 | 4.48 | 0 | Hydrophobic |
C7M | CG2 | VAL- 487 | 3.51 | 0 | Hydrophobic |
C7M | CB | ALA- 523 | 4.04 | 0 | Hydrophobic |
C8 | CG | ARG- 571 | 3.92 | 0 | Hydrophobic |
C4' | CB | LEU- 627 | 4.42 | 0 | Hydrophobic |
C5' | CD1 | LEU- 627 | 3.97 | 0 | Hydrophobic |
O3' | O | GLY- 628 | 2.68 | 145.38 | H-Bond (Ligand Donor) |
O2' | N | GLY- 631 | 2.6 | 134.75 | H-Bond (Protein Donor) |
O2 | N | LEU- 632 | 2.62 | 133.46 | H-Bond (Protein Donor) |
O2P | O | HOH- 715 | 2.81 | 179.98 | H-Bond (Protein Donor) |
O3B | O | HOH- 734 | 3.14 | 163.39 | H-Bond (Ligand Donor) |
O1P | O | HOH- 735 | 2.95 | 179.97 | H-Bond (Protein Donor) |
O1A | O | HOH- 737 | 2.78 | 179.97 | H-Bond (Protein Donor) |
O2P | O | HOH- 752 | 2.87 | 163.13 | H-Bond (Protein Donor) |