X-ray structure of nika in complex with FE(1S,2S)-N,N-kappa-BIS(2- pyridylmethyl)-N-carboxymethyl-N-kappa-methyl-1,2-cyclohexanediamine

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).

Ligands and binding sites

• L2M · {(R)-N-[(1S,2S)-2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}cyclohexyl]-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+) · ligand · 2 copies · chains A, B
• UNX · Unknown atom or ion · ion · 2 copies · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• ACT · Acetate ion · additive · 20 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

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

Interfaces

1 interface between chains.

• A–B · 1598 Ų buried · 19 hydrogen bonds · protein-protein

Compared structures

• 4DCY · X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2-pyridylmethyl)-N-carboxy… · 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 0.95

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 4DCY · PDBe 4DCY · UniProt P33590