A cytochrome C plus calixarene structure - alternative ligand binding mode

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 2% strand (DSSP).

Ligands and binding sites

• T3Y · 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9, 13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12, 15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid · ligand · 3 copies · chains A, B
• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• GOL · Glycerol · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 499 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (heme attachment).

Compared structures

• 4YE1 · A cytochrome c plus calixarene structure - alternative ligand binding mode · the same entry in another collection · chain A against A, TM-score 1.00
• P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P00044
• Elsewhere: RCSB PDB 4YE1 · PDBe 4YE1 · UniProt P00044