Ni-bound crystal structure of the engineered cyt CB562 variant, DICYT2, crystallized in the presence of CU(II) (M1) and NI(II) (M2)

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Ligands and binding sites

• HEC · Heme C · ligand · 2 copies · chains C, A
• NI · Nickel (II) ion · metal · 2 copies · chains C, A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• C–A · 446 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 1 disulfide (heme c attachment, disulfide).

Compared structures

• 7LRA · Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in… · the same entry in another collection · chain C against C, TM-score 1.00
• P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain C 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 P0ABE7
• Elsewhere: RCSB PDB 7LRA · PDBe 7LRA · UniProt P0ABE7