Crystal structure of the complex of three phase partition treated lipase from thermomyces lanuginosa with lauric acid and P- nitrobenzaldehyde (pnb) at 2.1 resolution

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Ligands and binding sites

• DAO · Lauric acid · ligand · 2 copies · chains A, B
• XXH · 4-nitrobenzaldehyde · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
• GOL · Glycerol · additive · 6 copies · chains A, B
• ACT · Acetate ion · additive · chains A
• EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 577 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 4KJX · Crystal Structure of the complex of three phase partition treated lipase from Thermomyces… · the same entry in another collection · chain A against A, TM-score 1.00
• O59952 · AlphaFold monomer V2.0 prediction for lipase (O59952) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O59952
• Elsewhere: RCSB PDB 4KJX · PDBe 4KJX · UniProt O59952