Crystal structure of tetrameric beta-2-microglobulin DELTAN6 S52C stabilized by a covalent ligand

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 56% strand (DSSP).

Ligands and binding sites

• SJK · 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1, 3]thiazolo[3,2-a]pyrimidine-6-carboxamide · ligand · 2 copies · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 393 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7AFV · Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a… · the same entry in another collection · chain A against A, TM-score 1.00
• P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P61769
• Elsewhere: RCSB PDB 7AFV · PDBe 7AFV · UniProt P61769