2.500 Å
X-ray
2004-05-14
Name: | Malonate-semialdehyde dehydrogenase |
---|---|
ID: | IOLA_BACSU |
AC: | P42412 |
Organism: | Bacillus subtilis |
Reign: | Bacteria |
TaxID: | 224308 |
EC Number: | 1.2.1.27 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 26.928 |
---|---|
Number of residues: | 48 |
Including | |
Standard Amino Acids: | 46 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.753 | 580.500 |
% Hydrophobic | % Polar |
---|---|
54.65 | 45.35 |
According to VolSite |
HET Code: | NAD |
---|---|
Formula: | C21H26N7O14P2 |
Molecular weight: | 662.417 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 70.42 % |
Polar Surface area: | 343.54 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 18 |
H-Bond Donors: | 6 |
Rings: | 5 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 1 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 11 |
X | Y | Z |
---|---|---|
83.1582 | -18.0934 | -4.29432 |
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 |
C1B | CG2 | ILE- 149 | 4.26 | 0 | Hydrophobic |
C4B | CG2 | ILE- 149 | 3.68 | 0 | Hydrophobic |
O3B | O | ALA- 150 | 2.67 | 154.47 | H-Bond (Ligand Donor) |
C5B | CB | PRO- 151 | 4.4 | 0 | Hydrophobic |
C5D | CB | PRO- 151 | 4.42 | 0 | Hydrophobic |
C5N | CG | PRO- 151 | 3.67 | 0 | Hydrophobic |
O2N | N | PHE- 152 | 3.22 | 137.24 | H-Bond (Protein Donor) |
C5D | CE2 | PHE- 152 | 4.01 | 0 | Hydrophobic |
C5N | CG2 | VAL- 158 | 4.21 | 0 | Hydrophobic |
O2B | NZ | LYS- 176 | 3.14 | 144.79 | H-Bond (Protein Donor) |
O2B | OE1 | GLU- 179 | 2.77 | 151.29 | H-Bond (Ligand Donor) |
DuAr | DuAr | HIS- 209 | 3.94 | 0 | Aromatic Face/Face |
C1B | CG2 | VAL- 212 | 4.44 | 0 | Hydrophobic |
C5B | CZ | PHE- 226 | 4.16 | 0 | Hydrophobic |
C4B | CE1 | PHE- 226 | 3.8 | 0 | Hydrophobic |
C1B | CE1 | PHE- 226 | 4.49 | 0 | Hydrophobic |
C4N | CG1 | VAL- 227 | 3.24 | 0 | Hydrophobic |
O1A | OG | SER- 229 | 2.69 | 161.28 | H-Bond (Protein Donor) |
O1A | N | SER- 229 | 2.93 | 151.7 | H-Bond (Protein Donor) |
O3 | N | SER- 229 | 3.46 | 143.17 | H-Bond (Protein Donor) |
C4D | CB | SER- 229 | 4.44 | 0 | Hydrophobic |
N7N | O | THR- 251 | 3.14 | 137.41 | H-Bond (Ligand Donor) |
C2D | CB | CYS- 284 | 4.27 | 0 | Hydrophobic |
C5N | SG | CYS- 284 | 3.81 | 0 | Hydrophobic |
C3N | CB | CYS- 284 | 3.33 | 0 | Hydrophobic |
O3D | OE2 | GLU- 382 | 2.79 | 149.8 | H-Bond (Ligand Donor) |
O2D | OE1 | GLU- 382 | 2.65 | 152.99 | H-Bond (Ligand Donor) |
C5D | CE1 | PHE- 384 | 3.62 | 0 | Hydrophobic |
C4D | CZ | PHE- 384 | 4.23 | 0 | Hydrophobic |
C2D | CE2 | PHE- 384 | 3.42 | 0 | Hydrophobic |
O2N | O | HOH- 2514 | 2.64 | 179.95 | H-Bond (Protein Donor) |
O3D | O | HOH- 2592 | 3.46 | 124.83 | H-Bond (Protein Donor) |