Crystal structure of human tyrosinase related protein 1 in complex with kojic acid

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 12% strand (DSSP).

Ligands and binding sites

• KOJ · 5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, C, B, D
• FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B, C, D
• MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, D
• ZN · Zinc ion · metal · 9 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, 10 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 452 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 331 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 328 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 233 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 192 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide, 22 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

• 5M8M · Crystal structure of human tyrosinase related protein 1 in complex with kojic acid · the same entry in another collection · chain A against A, TM-score 1.00
• P17643 · AlphaFold monomer V2.0 prediction for 5,6-dihydroxyindole-2-carboxylic acid oxidase… · a predicted model of the same protein · 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 P17643
• Elsewhere: RCSB PDB 5M8M · PDBe 5M8M · UniProt P17643