Lipidic sponge phase crystal structure of the photosynthetic reaction centre from blastochloris viridis (low dose)

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).

Ligands and binding sites

• HEC · Heme C · ligand · 4 copies · chains C, L, M
• BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
• MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 3 copies · chains L, M
• BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
• DGA · Diacyl glycerol · ligand · chains C, L, M
• MQ7 · Menaquinone-7 · ligand · chains L, M
• NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
• FE2 · Fe (II) ion · metal · chains L, M
• PO4 · Phosphate ion · ion · 2 copies · chains M, H, L

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• L–M · 4412 Ų buried · 62 hydrogen bonds · protein-protein
• H–M · 2870 Ų buried · 46 hydrogen bonds · protein-protein
• C–M · 2736 Ų buried · 34 hydrogen bonds · protein-protein
• H–L · 1788 Ų buried · 23 hydrogen bonds · protein-protein
• C–L · 1782 Ų buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 1 covalent, 1 modified (heme c attachment, covalent ligand, formylation).

Compared structures

• 2WJM · Lipidic sponge phase crystal structure of the photosynthetic reaction centre from… · the same entry in another collection · chain M against M, TM-score 1.00
• P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
• P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain L against A, TM-score 0.99
• P06010 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P06010) · a predicted model of the same protein · chain M against A, TM-score 0.98
• P06008 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P06008) · a predicted model of the same protein · chain H against A, TM-score 0.95

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 P07173
• Every structure of UniProt P06008
• Every structure of UniProt P06009
• Every structure of UniProt P06010
• Elsewhere: RCSB PDB 2WJM · PDBe 2WJM · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010