Holo-NI(II) hpnikr is a symmetric tetramer containing four canonic square-planar NI(II) ions at physiological pH

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 43% strand (DSSP).

Ligands and binding sites

• NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 933 Ų buried · 17 hydrogen bonds · protein-protein
• C–D · 887 Ų buried · 18 hydrogen bonds · protein-protein
• A–D · 728 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 703 Ų buried · 2 hydrogen bonds · protein-protein
• B–D · 102 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 2Y3Y · Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II)… · the same entry in another collection · chain B against B, TM-score 1.00
• B5Z8Y5 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (B5Z8Y5) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 B5Z8Y5
• Elsewhere: RCSB PDB 2Y3Y · PDBe 2Y3Y · UniProt B5Z8Y5