X-ray structure of nika in complex with fe-N,N'-BIS(2-pyridylmethyl)- N-carboxymethyl-N'-methyl

Structure

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

Ligands and binding sites

• L4D · {(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+) · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A
• ACT · Acetate ion · additive · 25 copies · chains A, B
• GOL · Glycerol · additive · 21 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 · 1627 Ų buried · 22 hydrogen bonds · protein-protein

Compared structures

• 4I9D · X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-me… · 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 0.95

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 4I9D · PDBe 4I9D · UniProt P33590