1.500 Å
X-ray
2008-07-14
Name: | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] |
---|---|
ID: | PCKGC_RAT |
AC: | P07379 |
Organism: | Rattus norvegicus |
Reign: | Eukaryota |
TaxID: | 10116 |
EC Number: | 4.1.1.32 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 6.278 |
---|---|
Number of residues: | 48 |
Including | |
Standard Amino Acids: | 41 |
Non Standard Amino Acids: | 2 |
Water Molecules: | 5 |
Cofactors: | |
Metals: | MN MN |
Ligandability | Volume (Å3) |
---|---|
0.536 | 617.625 |
% Hydrophobic | % Polar |
---|---|
48.09 | 51.91 |
According to VolSite |
HET Code: | GTP |
---|---|
Formula: | C10H12N5O14P3 |
Molecular weight: | 519.149 g/mol |
DrugBank ID: | DB04137 |
Buried Surface Area: | 70.98 % |
Polar Surface area: | 335.56 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 4 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
-4.18038 | -2.22956 | 22.6173 |
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 |
O2G | N | ALA- 287 | 2.97 | 146.85 | H-Bond (Protein Donor) |
O3B | N | ALA- 287 | 2.81 | 135.24 | H-Bond (Protein Donor) |
C5' | CB | ALA- 287 | 4.1 | 0 | Hydrophobic |
O2B | N | CYS- 288 | 3.4 | 139.94 | H-Bond (Protein Donor) |
O2B | N | GLY- 289 | 3.05 | 129.1 | H-Bond (Protein Donor) |
O3A | N | GLY- 289 | 3 | 148.61 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 290 | 2.85 | 151.48 | H-Bond (Protein Donor) |
O2B | N | LYS- 290 | 2.78 | 157.19 | H-Bond (Protein Donor) |
O2B | NZ | LYS- 290 | 2.81 | 157.9 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 290 | 2.85 | 0 | Ionic (Protein Cationic) |
O2B | NZ | LYS- 290 | 2.81 | 0 | Ionic (Protein Cationic) |
O1B | N | THR- 291 | 2.86 | 157.59 | H-Bond (Protein Donor) |
O2A | ND2 | ASN- 292 | 2.92 | 169.47 | H-Bond (Protein Donor) |
O2A | N | ASN- 292 | 2.97 | 159.77 | H-Bond (Protein Donor) |
C5' | CB | VAL- 335 | 4.28 | 0 | Hydrophobic |
C3' | CG1 | VAL- 335 | 4.17 | 0 | Hydrophobic |
O3' | O | PRO- 337 | 2.76 | 175.18 | H-Bond (Ligand Donor) |
O1G | NH1 | ARG- 405 | 3 | 151.5 | H-Bond (Protein Donor) |
O2G | NH2 | ARG- 405 | 2.94 | 157.87 | H-Bond (Protein Donor) |
O2G | NH1 | ARG- 405 | 3.37 | 135.43 | H-Bond (Protein Donor) |
O2G | CZ | ARG- 405 | 3.59 | 0 | Ionic (Protein Cationic) |
O6 | N | PHE- 530 | 2.98 | 173.77 | H-Bond (Protein Donor) |
C2' | CE1 | PHE- 530 | 4.14 | 0 | Hydrophobic |
O6 | ND2 | ASN- 533 | 3.17 | 148.26 | H-Bond (Protein Donor) |
O1G | MN | MN- 700 | 2.17 | 0 | Metal Acceptor |
O1B | MN | MN- 700 | 2.17 | 0 | Metal Acceptor |
O3G | MN | MN- 701 | 2.19 | 0 | Metal Acceptor |
N3 | O | HOH- 1227 | 2.98 | 179.95 | H-Bond (Protein Donor) |