Axial ligand swapping in double mutant maintains intradiol-cleavage chemistry in protocatechuate 3,4-dioxygenase

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 31% strand (DSSP).

Ligands and binding sites

• DHY · 2-(3,4-dihydroxyphenyl)acetic acid · ligand · 3 copies · chains A, M, B, N, C, O
• FE · Fe (III) ion · metal · 3 copies · chains M, N, O
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, N, C
• CO3 · Carbonate ion · ion · chains M
• CL · Chloride ion · ion · chains O
• GOL · Glycerol · additive · 6 copies · chains A, B, N, C, O
• BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, N

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

Pockets

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

Interfaces

15 interfaces between chains.

• B–N · 3723 Ų buried · 67 hydrogen bonds · protein-protein
• C–O · 3718 Ų buried · 64 hydrogen bonds · protein-protein
• A–M · 3712 Ų buried · 68 hydrogen bonds · protein-protein
• M–N · 342 Ų buried · 5 hydrogen bonds · protein-protein
• N–O · 339 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 3MFL · Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in… · the same entry in another collection · chain O against O, 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 M 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 3MFL · PDBe 3MFL · UniProt P00436 · UniProt P00437