Research workbench
Lhcii-2 in the state transition supercomplex psi-lhci-lhcii from the LHCBM1 lacking mutant of chlamydomonas reinhardti
Analyse Lhcii-2 in the state transition supercomplex psi-lhci-lhcii from the LHCBM1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E0I
- Type
- protein
- Length
- 677 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein, chloroplastic
- UniProt
- Q93WL4, Q9ZSJ4, Q93WE0
- Ligands
- CLA, CHL, LUT, XAT, NEX, LHG, LMG
- Pockets
- 15 · best druggability 0.71
Structure
electron microscopy · 3 distinct chains · 49% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 49% helix, 1% strand | Q93WL4 |
| V | Chlorophyll a-B binding protein, chloroplastic | protein | 238 | 48% helix, 2% strand | Q9ZSJ4 |
| W | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 49% helix, 1% strand | Q93WE0 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 24 copies · chains U, V, W
- CHL · Chlorophyll B · ligand · 18 copies · chains U, W, V
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains U, V, W
- 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 U, V, W
- 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 U, V, W
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 3 copies · chains U, V, W
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.71 | 0.77 | 74 | CLA, CHL |
| 2 | 375 | 0.60 | 0.76 | 37 | CHL, CLA |
| 3 | 279 | 0.58 | 0.77 | 31 | CLA |
| 4 | 280 | 0.56 | 0.77 | 34 | CHL, CLA |
| 5 | 106 | 0.54 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- U–W · 911 Ų buried · 7 hydrogen bonds · protein-protein
- U–V · 901 Ų buried · 6 hydrogen bonds · protein-protein
- V–W · 877 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7E0I · LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking… · the same entry in another collection · chain U against U, 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 Q93WL4
- Every structure of UniProt Q9ZSJ4
- Every structure of UniProt Q93WE0
- Elsewhere: RCSB PDB 7E0I · PDBe 7E0I · UniProt Q93WL4 · UniProt Q9ZSJ4 · UniProt Q93WE0
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