2.000 Å
X-ray
2005-03-04
Name: | Malate dehydrogenase |
---|---|
ID: | MDH_THETH |
AC: | P10584 |
Organism: | Thermus thermophilus |
Reign: | Bacteria |
TaxID: | 274 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 13.964 |
---|---|
Number of residues: | 35 |
Including | |
Standard Amino Acids: | 31 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 4 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.703 | 587.250 |
% Hydrophobic | % Polar |
---|---|
29.89 | 70.11 |
According to VolSite |
HET Code: | NAD |
---|---|
Formula: | C21H26N7O14P2 |
Molecular weight: | 662.417 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 48.46 % |
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 |
---|---|---|
23.2809 | 26.6983 | 25.1585 |
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 |
O2A | N | GLN- 14 | 2.89 | 172.28 | H-Bond (Protein Donor) |
O2N | N | ILE- 15 | 2.94 | 171.46 | H-Bond (Protein Donor) |
C5N | CD1 | ILE- 15 | 3.93 | 0 | Hydrophobic |
C5D | CD1 | ILE- 15 | 3.72 | 0 | Hydrophobic |
C5D | CG1 | VAL- 86 | 3.93 | 0 | Hydrophobic |
C3N | CG1 | VAL- 128 | 4.07 | 0 | Hydrophobic |
N7N | O | VAL- 128 | 3.33 | 169.82 | H-Bond (Ligand Donor) |
O3D | N | ASN- 130 | 3.04 | 153.44 | H-Bond (Protein Donor) |
O2D | ND2 | ASN- 130 | 2.92 | 152.17 | H-Bond (Protein Donor) |
C3N | CE | MET- 154 | 4.26 | 0 | Hydrophobic |
N7N | O | MET- 154 | 3.32 | 174.05 | H-Bond (Ligand Donor) |
C4N | CD2 | LEU- 157 | 3.74 | 0 | Hydrophobic |
O1N | OG | SER- 240 | 3.24 | 129.77 | H-Bond (Protein Donor) |
C4N | CB | ALA- 245 | 3.68 | 0 | Hydrophobic |
O2N | O | HOH- 1352 | 3.15 | 142.1 | H-Bond (Protein Donor) |
O7N | O | HOH- 1382 | 2.71 | 159.57 | H-Bond (Protein Donor) |