1.780 Å
X-ray
2005-02-28
Name: | Ras-related protein Rab-6A |
---|---|
ID: | RAB6A_HUMAN |
AC: | P20340 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 24.259 |
---|---|
Number of residues: | 39 |
Including | |
Standard Amino Acids: | 36 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 2 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.286 | 415.125 |
% Hydrophobic | % Polar |
---|---|
43.09 | 56.91 |
According to VolSite |
HET Code: | GNP |
---|---|
Formula: | C10H13N6O13P3 |
Molecular weight: | 518.164 g/mol |
DrugBank ID: | DB02082 |
Buried Surface Area: | 81.73 % |
Polar Surface area: | 338.36 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 16 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
24.7726 | 17.392 | 14.1697 |
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 |
C5' | CB | SER- 23 | 4.07 | 0 | Hydrophobic |
O1B | N | GLY- 25 | 2.99 | 148.93 | H-Bond (Protein Donor) |
O3A | N | GLY- 25 | 3.14 | 124.8 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 26 | 2.66 | 155.97 | H-Bond (Protein Donor) |
O1B | NZ | LYS- 26 | 2.84 | 151.1 | H-Bond (Protein Donor) |
O1B | N | LYS- 26 | 2.96 | 151.06 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 26 | 2.66 | 0 | Ionic (Protein Cationic) |
O1B | NZ | LYS- 26 | 2.84 | 0 | Ionic (Protein Cationic) |
O2B | N | THR- 27 | 3.05 | 162.73 | H-Bond (Protein Donor) |
O1A | N | SER- 28 | 2.88 | 139.18 | H-Bond (Protein Donor) |
O1A | OG | SER- 28 | 2.72 | 162.58 | H-Bond (Protein Donor) |
C2' | CZ | PHE- 38 | 3.98 | 0 | Hydrophobic |
O2' | O | ASP- 39 | 2.79 | 153.99 | H-Bond (Ligand Donor) |
O3' | O | ASN- 40 | 2.87 | 149.88 | H-Bond (Ligand Donor) |
O1G | OH | TYR- 42 | 2.52 | 172.7 | H-Bond (Protein Donor) |
C3' | CB | TYR- 42 | 3.83 | 0 | Hydrophobic |
C5' | CD1 | TYR- 42 | 3.6 | 0 | Hydrophobic |
O2G | N | THR- 45 | 3.13 | 154.32 | H-Bond (Protein Donor) |
O3G | N | GLY- 71 | 2.78 | 138.39 | H-Bond (Protein Donor) |
N7 | ND2 | ASN- 126 | 3.16 | 145.92 | H-Bond (Protein Donor) |
O4' | NZ | LYS- 127 | 3.11 | 131.82 | H-Bond (Protein Donor) |
N1 | OD2 | ASP- 129 | 2.74 | 175.98 | H-Bond (Ligand Donor) |
N1 | OD1 | ASP- 129 | 3.49 | 130.75 | H-Bond (Ligand Donor) |
N2 | OD1 | ASP- 129 | 2.73 | 159.25 | H-Bond (Ligand Donor) |
O6 | N | LYS- 158 | 3.21 | 160.94 | H-Bond (Protein Donor) |
O2G | MG | MG- 901 | 1.82 | 0 | Metal Acceptor |
O2B | MG | MG- 901 | 2.05 | 0 | Metal Acceptor |
O1G | O | HOH- 942 | 2.59 | 146.85 | H-Bond (Protein Donor) |