Research workbench
LHCII-1 in the state transition supercomplex PSI-LHCI-LHCII from the double phosphatase mutant pph1;pbcp of Chlamydomonas reinhardti.
Analyse LHCII-1 in the state transition supercomplex PSI-LHCI-LHCII from the double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E0J
- Type
- protein
- Length
- 672 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.13
- Source
- Chlamydomonas reinhardtii
- Molecule
- Chlorophyll a-b binding protein, chloroplastic
- UniProt
- Q93WE0, Q93WL4, Q93VE0
- Ligands
- CLA, CHL, LUT, XAT, NEX, LHG
- Pockets
- 19 · best druggability 0.59
Structure
electron microscopy · resolution 3.13 · 3 distinct chains · 51% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Chlorophyll a-b binding protein, chloroplastic | protein | 220 | 52% helix, 2% strand | Q93WE0 |
| Y | Chlorophyll a-b binding protein, chloroplastic | protein | 220 | 52% helix, 2% strand | Q93WL4 |
| Z | Chlorophyll a-b binding protein, chloroplastic | protein | 232 | 49% helix, 1% strand | Q93VE0 |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.59 | 0.87 | 21 | empty |
| 2 | 301 | 0.57 | 0.76 | 33 | CHL, CLA |
| 3 | 318 | 0.56 | 0.75 | 39 | CHL, CLA |
| 4 | 274 | 0.55 | 0.76 | 33 | CHL, CLA |
| 5 | 240 | 0.55 | 0.77 | 22 | CLA |
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
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