Crystal structure of the light-harvesting complex II (B800-850) from rhodospirillum molischianum

Structure

x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).

Ligands and binding sites

• HTO · Heptane-1,2,3-triol · ligand · 24 copies · chains A, D, B, J, E, G, H, K
• BCL · Bacteriochlorophyll A · ligand · 12 copies · chains A, B, D, E, G, H, J, K
• DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · 12 copies · chains A, B, D, E, G, H, J, K
• LYC · Lycopene · ligand · 4 copies · chains A, B, D, E, G, H, J, K

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

Pockets

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

Interfaces

14 interfaces between chains.

• D–E · 669 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 665 Ų buried · 6 hydrogen bonds · protein-protein
• G–H · 664 Ų buried · 6 hydrogen bonds · protein-protein
• J–K · 663 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 574 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 1LGH · Crystal structure of the light-harvesting complex II (B800-850) from rhodospirillum… · the same entry in another collection · chain K against K, TM-score 1.00
• P95673 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-800/850 beta 1 chain… · a predicted model of the same protein · chain B against A, TM-score 0.94
• P97253 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-800/850 alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P97253
• Every structure of UniProt P95673
• Elsewhere: RCSB PDB 1LGH · PDBe 1LGH · UniProt P97253 · UniProt P95673