Crystal structure of photosynthetic reaction center from a thermophilic bacterium, thermochromatium tepidum

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 8% strand (DSSP).

Ligands and binding sites

• BGL · 2-O-octyl-beta-D-glucopyranose · ligand · 6 copies · chains L, M, H, C
• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
• BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
• BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
• MQ8 · Menaquinone 8 · ligand · chains L, M
• CRT · Spirilloxanthin · ligand · chains M
• PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · chains L, M, H
• FE · Fe (III) ion · metal · chains L, M
• LDA · Lauryl dimethylamine-N-oxide · additive · chains L

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• L–M · 4552 Ų buried · 52 hydrogen bonds · protein-protein
• M–H · 2667 Ų buried · 36 hydrogen bonds · protein-protein
• C–M · 1968 Ų buried · 26 hydrogen bonds · protein-protein
• L–H · 1698 Ų buried · 22 hydrogen bonds · protein-protein
• C–L · 1409 Ų buried · 22 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1EYS · Crystal structure of photosynthetic reaction center from a thermophilic bacterium… · the same entry in another collection · chain C against C, 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 Q93RD8
• Elsewhere: RCSB PDB 1EYS · PDBe 1EYS · UniProt Q93RD8