2.000 Å
X-ray
2014-11-13
Name: | Serine hydroxymethyltransferase |
---|---|
ID: | GLYA_STRT1 |
AC: | Q5M0B4 |
Organism: | Streptococcus thermophilus |
Reign: | Bacteria |
TaxID: | 299768 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 24 % |
C | 76 % |
B-Factor: | 33.398 |
---|---|
Number of residues: | 49 |
Including | |
Standard Amino Acids: | 46 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 3 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.668 | 712.125 |
% Hydrophobic | % Polar |
---|---|
34.60 | 65.40 |
According to VolSite |
HET Code: | 2BO |
---|---|
Formula: | C12H17N2O8P |
Molecular weight: | 348.246 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 75.49 % |
Polar Surface area: | 192.32 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 9 |
H-Bond Donors: | 3 |
Rings: | 1 |
Aromatic rings: | 1 |
Anionic atoms: | 3 |
Cationic atoms: | 1 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
-11.7123 | -64.4074 | -11.6517 |
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 |
O | OG | SER- 29 | 2.77 | 146.38 | H-Bond (Protein Donor) |
O1P | OH | TYR- 49 | 2.59 | 161.33 | H-Bond (Protein Donor) |
O4P | OH | TYR- 49 | 3.39 | 126.85 | H-Bond (Protein Donor) |
OB | OE2 | GLU- 51 | 2.79 | 125.52 | H-Bond (Ligand Donor) |
O | OH | TYR- 59 | 2.74 | 157.94 | H-Bond (Protein Donor) |
CG | CZ | TYR- 59 | 4.36 | 0 | Hydrophobic |
O2P | N | GLY- 92 | 2.93 | 157.85 | H-Bond (Protein Donor) |
O3P | OG | SER- 93 | 2.63 | 162.38 | H-Bond (Protein Donor) |
O3P | N | SER- 93 | 2.99 | 153.46 | H-Bond (Protein Donor) |
C2A | CB | HIS- 120 | 4.15 | 0 | Hydrophobic |
C3 | CB | HIS- 120 | 4.35 | 0 | Hydrophobic |
DuAr | DuAr | HIS- 120 | 3.61 | 0 | Aromatic Face/Face |
O3 | OG | SER- 170 | 2.73 | 156.58 | H-Bond (Protein Donor) |
N1 | OD2 | ASP- 195 | 2.64 | 141.99 | H-Bond (Protein Donor) |
C2A | CB | ALA- 197 | 3.86 | 0 | Hydrophobic |
C3 | CB | ALA- 197 | 4.12 | 0 | Hydrophobic |
OT | NE2 | HIS- 198 | 2.64 | 158.67 | H-Bond (Protein Donor) |
C5A | CG2 | THR- 221 | 4.41 | 0 | Hydrophobic |
O2P | NE2 | HIS- 223 | 3.29 | 166.85 | H-Bond (Protein Donor) |
O1P | N | GLY- 256 | 2.9 | 171.69 | H-Bond (Protein Donor) |
O | NH2 | ARG- 357 | 3.06 | 176.92 | H-Bond (Protein Donor) |
OT | NH1 | ARG- 357 | 2.87 | 168.17 | H-Bond (Protein Donor) |
O | CZ | ARG- 357 | 3.88 | 0 | Ionic (Protein Cationic) |
OT | CZ | ARG- 357 | 3.7 | 0 | Ionic (Protein Cationic) |
O3P | O | HOH- 622 | 2.74 | 179.98 | H-Bond (Protein Donor) |