Structure of Y257F variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with 4-nitrocatechol and dioxygen at 1.67 ang resolution

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).

Ligands and binding sites

• 4NC · 4-nitrocatechol · ligand · 3 copies · chains A, C, D
• 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 · 2 copies · chains C, D
• P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D
• PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–D · 1682 Ų buried · 43 hydrogen bonds · protein-protein
• A–B · 1670 Ų buried · 35 hydrogen bonds · protein-protein
• C–D · 1666 Ų buried · 39 hydrogen bonds · protein-protein
• A–C · 1272 Ų buried · 37 hydrogen bonds · protein-protein
• B–C · 528 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 4GHF · Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in… · 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 4GHF · PDBe 4GHF · UniProt Q45135