Crystal structure of aaudyp complexed with imidazole

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• OXD · Oxalic acid · ligand · chains A
• GOA · Glycolic acid · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar
• K · Potassium ion · metal · 2 copies · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B
• ACT · Acetate ion · additive · 6 copies · chains A, B
• IMD · Imidazole · additive · 4 copies · chains A, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
• MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
• FMT · Formic acid · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 676 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan (N-glycosylation).

Compared structures

• 4UZI · Crystal Structure of AauDyP Complexed with Imidazole · the same entry in another collection · chain A against A, TM-score 1.00
• I2DBY1 · AlphaFold monomer V2.0 prediction for dye-decolorizing peroxidase AAUDYP1 (I2DBY1) · a predicted model of the same protein · chain B 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 I2DBY1
• Elsewhere: RCSB PDB 4UZI · PDBe 4UZI · UniProt I2DBY1