LHCII-1 in the state transition supercomplex PSI-LHCI-LHCII from the double phosphatase mutant pph1;pbcp of Chlamydomonas reinhardti.

Structure

electron microscopy · resolution 3.13 · 3 distinct chains · 51% helix, 1% strand (DSSP).

Ligands and binding sites

• CLA · Chlorophyll A · ligand · 24 copies · chains X, Y, Z
• CHL · Chlorophyll B · ligand · 17 copies · chains X, Z, Y
• LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains X, Y, Z
• 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 X, Y, Z
• 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 X, Y, Z
• LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 3 copies · chains X, Y, Z

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• X–Z · 941 Ų buried · 4 hydrogen bonds · protein-protein
• X–Y · 879 Ų buried · 3 hydrogen bonds · protein-protein
• Y–Z · 854 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

• 7E0J · Lhcii-1 in the state transition supercomplex psi-lhci-lhcii from the double phosphatase… · the same entry in another collection · chain X against X, 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 Q93WE0
• Every structure of UniProt Q93WL4
• Every structure of UniProt Q93VE0
• Elsewhere: RCSB PDB 7E0J · PDBe 7E0J · UniProt Q93WE0 · UniProt Q93WL4 · UniProt Q93VE0