Structure of homoprotocatechuate 2,3-dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).

Ligands and binding sites

• XX3 · (1S)-1-hydroperoxy-1-hydroxy-2-keto-5-nitrocyclohexa-3,5-diene · ligand · 2 copies · chains B, D
• XXP · 2-keto,5-nitro,6-hydroxy-3,5-hexadienoic acid · ligand · chains A
• XX2 · 1-keto,2-hydroxy,4-nitrobenzene, 1 electron oxidized · ligand · chains C
• FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · chains B
• CL · Chloride ion · ion · 4 copies · chains A, B, C, D
• OXY · Oxygen molecule · ion · chains C
• GOL · Glycerol · additive · 13 copies · chains A, C, B, D

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–D · 1699 Ų buried · 40 hydrogen bonds · protein-protein
• A–C · 1695 Ų buried · 45 hydrogen bonds · protein-protein
• A–B · 1687 Ų buried · 35 hydrogen bonds · protein-protein
• C–D · 1674 Ų buried · 38 hydrogen bonds · protein-protein
• B–C · 539 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 2IGA · Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q45135
• Elsewhere: RCSB PDB 2IGA · PDBe 2IGA · UniProt Q45135