Pea light-harvesting complex II at 2.5 ångström resolution

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 4% strand (DSSP).

Ligands and binding sites

• CLA · Chlorophyll A · ligand · 24 copies · chains A, C, B
• CHL · Chlorophyll B · ligand · 18 copies · chains A, C, B
• LUX · (3R,3'R,6'S,9R,9'R,13R,13'S)-4',5'-didehydro-5',6',7', 8',9,9',10,10',11,11',12,12',13,13',14,14',15,15'-octadecahydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains A, B, C
• NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 3 copies · chains A, B, C
• XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 3 copies · chains A, C, B
• LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 3 copies · chains A, B, C
• DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 3 copies · chains A, B, C

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

3 interfaces between chains.

• A–B · 777 Ų buried · 5 hydrogen bonds · protein-protein
• B–C · 774 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 774 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 2BHW · Pea light-harvesting complex II at 2.5 ångström resolution · the same entry in another collection · chain A against A, TM-score 1.00
• P07371 · AlphaFold monomer V2.0 prediction for chlorophyll a-B binding protein AB80, chloroplastic… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P07371
• Elsewhere: RCSB PDB 2BHW · PDBe 2BHW · UniProt P07371