A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Hexagonal Form

Structure

x-ray diffraction · resolution 3 · 1 distinct chain · 80% helix, 0% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• PXX · N-1,10-phenanthrolin-5-ylacetamide · ligand · 2 copies · chains A, B
• NI · Nickel (II) ion · metal · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 33 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 2 covalent (heme attachment, covalent ligand).

Compared structures

• 3FOP · A triangular cytochrome B562 superstructure mediated by ni coordination - hexagonal form · the same entry in another collection · chain A against A, TM-score 1.00
• P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 3FOP · PDBe 3FOP · UniProt P0ABE7