X-ray structure of nika from escherichia COLI in complex with RU(BIS(PYRZOL-1-YL)ACETATE SCORPIONATE)(CO)2CL

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).

Ligands and binding sites

• EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains A
• 6RP · bis(pyrzol-1-yl)acetate scorpionate · ligand · chains B
• FE · Fe (III) ion · metal · chains A
• RU · Ruthenium ion · metal · chains B
• CL · Chloride ion · ion · 2 copies · chains B
• CMO · Carbon monoxide · ion · 2 copies · chains B
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · 12 copies · chains A, B
• ACT · Acetate ion · additive · 10 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1611 Ų buried · 21 hydrogen bonds · protein-protein

Compared structures

• 5L8D · X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate… · the same entry in another collection · chain B against B, TM-score 1.00
• P33590 · AlphaFold monomer V2.0 prediction for nickel-binding periplasmic protein (P33590) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P33590
• Elsewhere: RCSB PDB 5L8D · PDBe 5L8D · UniProt P33590