Crystal structure of NikA in complex with hydroxylated Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)

Structure

x-ray diffraction · resolution 1.7 · 2 distinct chains · 31% helix, 24% strand (DSSP).

Ligands and binding sites

• 9YK · 2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid · ligand · 2 copies · chains A, B
• FE · Fe (III) ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 7 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · 13 copies · chains A, B
• ACT · Acetate ion · additive · 8 copies · chains A, B
• DTD · Dithiane diol · additive · 2 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 · 1542 Ų buried · 20 hydrogen bonds · protein-protein

Compared structures

• 5ON1 · Crystal structure of nika in complex with hydroxylated fe-L1 (N-(2… · 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 5ON1 · PDBe 5ON1 · UniProt P33590