2.300 Å
X-ray
2005-04-14
Name: | Glycogenin-1 |
---|---|
ID: | GLYG_RABIT |
AC: | P13280 |
Organism: | Oryctolagus cuniculus |
Reign: | Eukaryota |
TaxID: | 9986 |
EC Number: | 2.4.1.186 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 51.144 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 32 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 1 |
Cofactors: | |
Metals: | MN |
Ligandability | Volume (Å3) |
---|---|
0.104 | 442.125 |
% Hydrophobic | % Polar |
---|---|
40.46 | 59.54 |
According to VolSite |
HET Code: | UPG |
---|---|
Formula: | C15H22N2O17P2 |
Molecular weight: | 564.286 g/mol |
DrugBank ID: | DB01861 |
Buried Surface Area: | 59.43 % |
Polar Surface area: | 316.82 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 7 |
Rings: | 3 |
Aromatic rings: | 0 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 9 |
X | Y | Z |
---|---|---|
5.20061 | -37.0024 | 86.6142 |
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 |
C1C | CD2 | LEU- 8 | 4.16 | 0 | Hydrophobic |
O2C | O | LEU- 8 | 2.67 | 160.94 | H-Bond (Ligand Donor) |
N3 | OG1 | THR- 10 | 2.72 | 134.8 | H-Bond (Ligand Donor) |
O2 | N | THR- 10 | 2.93 | 137.13 | H-Bond (Protein Donor) |
C3C | CE2 | TYR- 14 | 3.58 | 0 | Hydrophobic |
C2C | CD2 | TYR- 14 | 3.49 | 0 | Hydrophobic |
C1C | CG1 | VAL- 81 | 4.18 | 0 | Hydrophobic |
O6' | OD2 | ASP- 101 | 3.1 | 173.4 | H-Bond (Ligand Donor) |
C3C | CB | ASP- 101 | 4.36 | 0 | Hydrophobic |
O2C | N | ALA- 102 | 3.02 | 154.01 | H-Bond (Protein Donor) |
O3C | N | ALA- 102 | 2.89 | 121.71 | H-Bond (Protein Donor) |
C2C | CB | ALA- 102 | 3.69 | 0 | Hydrophobic |
O3C | OD1 | ASP- 103 | 2.76 | 129.66 | H-Bond (Ligand Donor) |
O3C | N | ASP- 103 | 3.41 | 139.15 | H-Bond (Protein Donor) |
C4' | CB | GLN- 163 | 4.46 | 0 | Hydrophobic |
O4' | NE2 | GLN- 163 | 2.7 | 124.62 | H-Bond (Protein Donor) |
C5' | CD2 | LEU- 213 | 3.89 | 0 | Hydrophobic |
O1A | NZ | LYS- 217 | 3.73 | 0 | Ionic (Protein Cationic) |
O2A | NZ | LYS- 217 | 3.8 | 0 | Ionic (Protein Cationic) |
O2B | NZ | LYS- 217 | 2.91 | 0 | Ionic (Protein Cationic) |
O2B | NZ | LYS- 217 | 2.91 | 139.36 | H-Bond (Protein Donor) |
O1A | MN | MN- 400 | 2.5 | 0 | Metal Acceptor |
O1B | MN | MN- 400 | 1.9 | 0 | Metal Acceptor |
O6' | O | HOH- 440 | 2.71 | 143.94 | H-Bond (Protein Donor) |