A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Ligands and binding sites

• 4EY · 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium · ligand · 2 copies · chains B, C
• ENJ · (4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid · ligand · chains A
• NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 16 copies · chains A, B, C
• SO3 · Sulfite ion · ion · chains C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 484 Ų buried · 5 hydrogen bonds · protein-protein
• B–C · 473 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 174 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

• 6C1W · A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in… · the same entry in another collection · chain A against A, TM-score 1.00
• F9USS9 · AlphaFold monomer V2.0 prediction for lactate racemase (F9USS9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 F9USS9
• Elsewhere: RCSB PDB 6C1W · PDBe 6C1W · UniProt F9USS9