Crystal structure of trypanosoma brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).

Ligands and binding sites

• 9YB · (3~{R})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid · ligand · 4 copies · chains A, D, B, C
• SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
• BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 283 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 282 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 267 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 26 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

• 5OML · Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small… · 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 Q8IEW2
• Elsewhere: RCSB PDB 5OML · PDBe 5OML · UniProt Q8IEW2