X-ray structure of nika in complex with FE(1R,2R)-N,N'-BIS(2- pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).

Ligands and binding sites

• L2D · {2,2'-[(1R,2R)-cyclohexane-1,2-diylbis{[(pyridin-2-yl-kappaN)methyl]imino-kappaN}]diacetato-kappaO(2-)}iron · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, B
• ACT · Acetate ion · additive · 27 copies · chains A, B
• GOL · Glycerol · additive · 18 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1583 Ų buried · 22 hydrogen bonds · protein-protein

Compared structures

• 4DCX · X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxy… · the same entry in another collection · chain A against A, 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 4DCX · PDBe 4DCX · UniProt P33590