Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).

Ligands and binding sites

• 4UD · (2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid · ligand · 2 copies · chains A, C, B, D
• EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, C, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–C · 5886 Ų buried · 113 hydrogen bonds · protein-protein
• B–D · 5842 Ų buried · 112 hydrogen bonds · protein-protein
• C–B · 456 Ų buried · 6 hydrogen bonds · protein-protein
• C–D · 451 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 438 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 5BPK · Varying binding modes of inhibitors and structural differences in the binding pockets of… · 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 O25743
• Elsewhere: RCSB PDB 5BPK · PDBe 5BPK · UniProt O25743