4-fluorocatechol bound to protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 30% strand (DSSP).

Ligands and binding sites

• 3N8 · 4-fluorobenzene-1,2-diol · ligand · 10 copies · chains A, F, E, D, C, B
• MUC · [(2S)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid · ligand · 2 copies · chains E, C
• FE · Fe (III) ion · metal · 3 copies · chains F, D, B
• CL · Chloride ion · ion · 3 copies · chains F, B
• SO4 · Sulfate ion · ion · chains A
• BME · Beta-mercaptoethanol · additive · 4 copies · chains A, F, C, D, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

15 interfaces between chains.

• F–E · 3698 Ų buried · 67 hydrogen bonds · protein-protein
• C–D · 3698 Ų buried · 69 hydrogen bonds · protein-protein
• A–B · 3668 Ų buried · 67 hydrogen bonds · protein-protein
• F–D · 338 Ų buried · 6 hydrogen bonds · protein-protein
• F–B · 334 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

• 4WHS · 4-fluorocatechol bound to Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5 · the same entry in another collection · chain B against B, TM-score 1.00
• P00437 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase beta chain (P00437) · a predicted model of the same protein · chain F against A, TM-score 1.00
• P00436 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase alpha chain (P00436) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P00436
• Every structure of UniProt P00437
• Elsewhere: RCSB PDB 4WHS · PDBe 4WHS · UniProt P00436 · UniProt P00437