2.100 Å
X-ray
2008-12-17
Name: | NtrC-like two-domain protein |
---|---|
ID: | D0VX10_9FIRM |
AC: | D0VX10 |
Organism: | [Eubacterium] rectale |
Reign: | Bacteria |
TaxID: | 39491 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 31.481 |
---|---|
Number of residues: | 31 |
Including | |
Standard Amino Acids: | 28 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 2 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.026 | 253.125 |
% Hydrophobic | % Polar |
---|---|
46.67 | 53.33 |
According to VolSite |
HET Code: | ATP |
---|---|
Formula: | C10H12N5O13P3 |
Molecular weight: | 503.149 g/mol |
DrugBank ID: | DB00171 |
Buried Surface Area: | 52.66 % |
Polar Surface area: | 319.88 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
2.54316 | 49.8649 | 24.8261 |
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 |
O1G | N | GLY- 135 | 2.87 | 163.75 | H-Bond (Protein Donor) |
O2B | N | GLY- 137 | 2.99 | 150.29 | H-Bond (Protein Donor) |
O3A | N | GLY- 137 | 3.23 | 121.59 | H-Bond (Protein Donor) |
O2B | N | THR- 138 | 3.11 | 140.19 | H-Bond (Protein Donor) |
O1B | N | SER- 139 | 2.89 | 163.82 | H-Bond (Protein Donor) |
O2A | OG1 | THR- 140 | 2.71 | 160.76 | H-Bond (Protein Donor) |
O2A | N | THR- 140 | 2.86 | 144.14 | H-Bond (Protein Donor) |
N7 | ND2 | ASN- 307 | 3 | 168.19 | H-Bond (Protein Donor) |
N6 | OD1 | ASN- 307 | 2.89 | 136.15 | H-Bond (Ligand Donor) |
N6 | O | PRO- 329 | 2.93 | 137.17 | H-Bond (Ligand Donor) |
N1 | N | TYR- 331 | 2.94 | 148.69 | H-Bond (Protein Donor) |
C1' | CD1 | ILE- 339 | 4.41 | 0 | Hydrophobic |
O2G | MG | MG- 501 | 1.99 | 0 | Metal Acceptor |
O1B | MG | MG- 501 | 2.21 | 0 | Metal Acceptor |