2.690 Å
X-ray
2010-10-28
Name: | Holliday junction ATP-dependent DNA helicase RuvB |
---|---|
ID: | RUVB_CAMJE |
AC: | Q9PMT7 |
Organism: | Campylobacter jejuni subsp. jejuni serotype O:2 |
Reign: | Bacteria |
TaxID: | 192222 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 7 % |
B | 93 % |
B-Factor: | 45.811 |
---|---|
Number of residues: | 27 |
Including | |
Standard Amino Acids: | 27 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.580 | 1022.625 |
% Hydrophobic | % Polar |
---|---|
40.92 | 59.08 |
According to VolSite |
HET Code: | ADP |
---|---|
Formula: | C10H12N5O10P2 |
Molecular weight: | 424.177 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 58.89 % |
Polar Surface area: | 260.7 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 14 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 3 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 6 |
X | Y | Z |
---|---|---|
12.7317 | 35.3026 | 151.823 |
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 |
N6 | OH | TYR- 28 | 3.3 | 125.31 | H-Bond (Ligand Donor) |
N6 | O | ILE- 29 | 2.82 | 138.12 | H-Bond (Ligand Donor) |
O3B | N | GLY- 62 | 2.75 | 143.87 | H-Bond (Protein Donor) |
O1B | N | GLY- 64 | 2.95 | 150.51 | H-Bond (Protein Donor) |
O3A | N | GLY- 64 | 3.19 | 123.21 | H-Bond (Protein Donor) |
O1B | NZ | LYS- 65 | 3.65 | 0 | Ionic (Protein Cationic) |
O1B | N | LYS- 65 | 2.86 | 167.99 | H-Bond (Protein Donor) |
O2B | OG1 | THR- 66 | 3.06 | 157.81 | H-Bond (Protein Donor) |
O2B | N | THR- 66 | 3.12 | 164.19 | H-Bond (Protein Donor) |
O1A | N | THR- 67 | 2.79 | 142.76 | H-Bond (Protein Donor) |
O1A | OG1 | THR- 67 | 3.09 | 171.27 | H-Bond (Protein Donor) |
N6 | OH | TYR- 181 | 3.3 | 132.73 | H-Bond (Ligand Donor) |
C1' | CB | PRO- 217 | 3.7 | 0 | Hydrophobic |
O3B | CZ | ARG- 218 | 3.7 | 0 | Ionic (Protein Cationic) |
C4' | CB | ARG- 218 | 4.3 | 0 | Hydrophobic |
C1' | CD2 | LEU- 221 | 3.61 | 0 | Hydrophobic |