Research workbench
Structure of M-lhcii and CP24 complexes in the stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum
Analyse Structure of M-lhcii and CP24 complexes in the stacked C2S2M2-type psii-lhcii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XNN
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein 8, chloroplastic; Chlorophyll a-B binding protein…
- UniProt
- P27490, Q04918
- Ligands
- CLA, CHL, LUT, XAT, LHG, NEX, BCR
- Pockets
- 20 · best druggability 0.66
Structure
electron microscopy · 4 distinct chains · 50% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Chlorophyll a-B binding protein 8, chloroplastic | protein | 219 | 53% helix, 2% strand | P27490 |
| 2 | Chlorophyll a-B binding protein 8, chloroplastic | protein | 218 | 49% helix, 3% strand | P27490 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 52% helix, 1% strand | Q04918 |
| 4 | Light harvesting chlorophyll A/B-binding protein LHCB6, CP24 | protein | 197 | 45% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 30 copies · chains 1, 3, 2, 4
- CHL · Chlorophyll B · ligand · 23 copies · chains 1, 2, 3, 4
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 7 copies · chains 1, 2, 3, 4
- 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 · 4 copies · chains 1, 2, 3, 4
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains 1, 2, 3, 4
- 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 1, 2, 3
- BCR · Beta-carotene · ligand · chains 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.66 | 0.79 | 39 | CHL, CLA |
| 2 | 265 | 0.59 | 0.79 | 31 | CLA |
| 3 | 218 | 0.59 | 0.80 | 21 | CLA |
| 4 | 296 | 0.58 | 0.77 | 34 | CHL, CLA |
| 5 | 244 | 0.58 | 0.79 | 38 | empty |
Interfaces
4 interfaces between chains.
- 1–3 · 894 Ų buried · 2 hydrogen bonds · protein-protein
- 2–3 · 809 Ų buried · 5 hydrogen bonds · protein-protein
- 1–2 · 774 Ų buried · 6 hydrogen bonds · protein-protein
- 3–4 · 444 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5XNN · Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII… · the same entry in another collection · chain 2 against 2, TM-score 1.00
- P27490 · AlphaFold monomer V2.0 prediction for chlorophyll a-B binding protein 8, chloroplastic… · a predicted model of the same protein · chain 1 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 P27490
- Every structure of UniProt Q04918
- Elsewhere: RCSB PDB 5XNN · PDBe 5XNN · UniProt P27490 · UniProt Q04918
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