Salmonella typhimurium D-cysteine desulfhydrase soaked with D-cys shows pyruvate bound 4 a away from active site

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).

Ligands and binding sites

• BEN · Benzamidine · ligand · 3 copies · chains A, B, C, D
• PYR · Pyruvic acid · ligand · 3 copies · chains A, C, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
• CL · Chloride ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains B, C

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 1538 Ų buried · 17 hydrogen bonds · protein-protein
• C–D · 1504 Ų buried · 15 hydrogen bonds · protein-protein
• B–C · 451 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 449 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 413 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

• 4D8W · Salmonella typhimurium D-Cysteine desulfhydrase soaked with D-cys shows pyruvate bound 4… · the same entry in another collection · chain D against D, TM-score 1.00
• Q8ZNT7 · AlphaFold monomer V2.0 prediction for D-cysteine desulfhydrase (Q8ZNT7) · 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 Q8ZNT7
• Elsewhere: RCSB PDB 4D8W · PDBe 4D8W · UniProt Q8ZNT7