Crystal structure of the cytochrome C-552 from hydrogenobacter thermophilus at 2.0 resolution

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 3% strand (DSSP).

Ligands and binding sites

• HEC · Heme C · ligand · 4 copies · chains A, D, B, C
• SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, D, C, 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, 1 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 415 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 409 Ų buried · 5 hydrogen bonds · protein-protein
• A–B · 392 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 299 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 285 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1YNR · Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0… · the same entry in another collection · chain C against C, TM-score 1.00
• P15452 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P15452) · 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 P15452
• Elsewhere: RCSB PDB 1YNR · PDBe 1YNR · UniProt P15452