1.560 Å
X-ray
2015-11-01
Name: | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase |
---|---|
ID: | MEND_ECOLI |
AC: | P17109 |
Organism: | Escherichia coli |
Reign: | Bacteria |
TaxID: | 83333 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
C | 69 % |
D | 31 % |
B-Factor: | 11.221 |
---|---|
Number of residues: | 54 |
Including | |
Standard Amino Acids: | 50 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 3 |
Cofactors: | |
Metals: | MN |
Ligandability | Volume (Å3) |
---|---|
1.255 | 1326.375 |
% Hydrophobic | % Polar |
---|---|
48.85 | 51.15 |
According to VolSite |
HET Code: | TD6 |
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Formula: | C16H21N4O10P2S |
Molecular weight: | 523.371 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 80.44 % |
Polar Surface area: | 285.67 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 13 |
H-Bond Donors: | 2 |
Rings: | 2 |
Aromatic rings: | 2 |
Anionic atoms: | 4 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 12 |
X | Y | Z |
---|---|---|
-48.3651 | 21.4105 | 10.7398 |
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 |
CM4 | CG | PRO- 30 | 3.61 | 0 | Hydrophobic |
N1' | OE1 | GLU- 55 | 2.89 | 158 | H-Bond (Ligand Donor) |
N1' | OE2 | GLU- 55 | 3.02 | 138.28 | H-Bond (Ligand Donor) |
C5' | CG2 | THR- 78 | 4.04 | 0 | Hydrophobic |
CM2 | CB | ALA- 82 | 4.37 | 0 | Hydrophobic |
OL3 | ND2 | ASN- 117 | 3.04 | 153.03 | H-Bond (Protein Donor) |
S1 | CB | SER- 391 | 3.62 | 0 | Hydrophobic |
C7 | CB | SER- 391 | 3.93 | 0 | Hydrophobic |
O1B | OG | SER- 391 | 2.54 | 162.71 | H-Bond (Protein Donor) |
OL2 | N | SER- 391 | 2.89 | 158.29 | H-Bond (Protein Donor) |
O2B | N | LEU- 392 | 2.97 | 150.35 | H-Bond (Protein Donor) |
OL2 | CZ | ARG- 395 | 3.7 | 0 | Ionic (Protein Cationic) |
OL3 | CZ | ARG- 395 | 3.51 | 0 | Ionic (Protein Cationic) |
OL2 | NH1 | ARG- 395 | 2.86 | 171.53 | H-Bond (Protein Donor) |
OL3 | NH2 | ARG- 395 | 2.7 | 173.68 | H-Bond (Protein Donor) |
OL3 | NH1 | ARG- 395 | 3.44 | 128.73 | H-Bond (Protein Donor) |
OL2 | CZ | ARG- 413 | 3.75 | 0 | Ionic (Protein Cationic) |
OL3 | CZ | ARG- 413 | 3.63 | 0 | Ionic (Protein Cationic) |
OL2 | NH2 | ARG- 413 | 2.78 | 166.03 | H-Bond (Protein Donor) |
OL3 | NH1 | ARG- 413 | 3.1 | 140.47 | H-Bond (Protein Donor) |
OL3 | NH2 | ARG- 413 | 3.34 | 132.72 | H-Bond (Protein Donor) |
C13 | CB | SER- 416 | 3.65 | 0 | Hydrophobic |
N4' | O | SER- 416 | 3.03 | 162.29 | H-Bond (Ligand Donor) |
S1 | CG2 | ILE- 418 | 4.41 | 0 | Hydrophobic |
C5' | CG1 | ILE- 418 | 4.17 | 0 | Hydrophobic |
CM2 | CG1 | ILE- 418 | 4.14 | 0 | Hydrophobic |
CM4 | CD1 | ILE- 418 | 3.73 | 0 | Hydrophobic |
C7 | CD1 | ILE- 418 | 4.06 | 0 | Hydrophobic |
N3' | N | ILE- 418 | 3.09 | 159.07 | H-Bond (Protein Donor) |
CM2 | CB | ASP- 419 | 3.65 | 0 | Hydrophobic |
C6 | CD1 | LEU- 443 | 4.32 | 0 | Hydrophobic |
C7 | CB | LEU- 443 | 4.16 | 0 | Hydrophobic |
O1A | N | LEU- 443 | 3.03 | 167.73 | H-Bond (Protein Donor) |
O2A | N | SER- 444 | 2.94 | 147.18 | H-Bond (Protein Donor) |
O2A | OG | SER- 444 | 2.74 | 163.6 | H-Bond (Protein Donor) |
CM2 | CE1 | TYR- 447 | 3.76 | 0 | Hydrophobic |
O3B | ND2 | ASN- 469 | 3.01 | 144.74 | H-Bond (Protein Donor) |
O3B | N | GLN- 473 | 2.97 | 158.31 | H-Bond (Protein Donor) |
S1 | CG2 | ILE- 474 | 3.77 | 0 | Hydrophobic |
C6 | CG2 | ILE- 474 | 4.42 | 0 | Hydrophobic |
CLB | CD1 | ILE- 474 | 4.37 | 0 | Hydrophobic |
O1B | N | ILE- 474 | 3.05 | 162.63 | H-Bond (Protein Donor) |
C6 | CE2 | PHE- 475 | 4.21 | 0 | Hydrophobic |
CM4 | CE2 | PHE- 475 | 4.22 | 0 | Hydrophobic |
O1A | MN | MN- 602 | 2.08 | 0 | Metal Acceptor |
O3B | MN | MN- 602 | 2.17 | 0 | Metal Acceptor |