Bimetallic dodecameric cage design 3 (BMC3) from cytochrome CB562

Structure

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

Ligands and binding sites

• HAE · Acetohydroxamic acid · ligand · 8 copies · chains D, C, A, B
• HEC · Heme C · ligand · 4 copies · chains D, A, B, C
• ZN · Zinc ion · metal · 7 copies · chains D, A, C, B
• FE · Fe (III) ion · metal · 4 copies · chains C
• 1PE · Pentaethylene glycol · additive · chains D, A, C

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–C · 427 Ų buried · 4 hydrogen bonds · protein-protein
• D–C · 422 Ų buried · 3 hydrogen bonds · protein-protein
• D–A · 420 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 384 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 143 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 8 covalent (heme c attachment, covalent ligand).

Compared structures

• 6OT7 · Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562 · 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 B 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 6OT7 · PDBe 6OT7 · UniProt P0ABE7