Research workbench
Barley photosystem I-lhci-LHCA6 supercomplex
Analyse Barley photosystem I-lhci-LHCA6 supercomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EWK
- Type
- protein
- Length
- 3,110 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- S4Z1K7, S4Z289, S4Z1D9, S4Z1E9, Q9LKC7
- Ligands
- CLA, BCR, CHL, LUT, LHG, SF4, PQN, DGD, LMG, XAT, CL0
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 15 distinct chains · 52% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 60% helix, 4% strand | S4Z1K7 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 58% helix, 2% strand | S4Z289 |
| C | Photosystem I iron-sulfur center | protein | 81 | 5% helix, 21% strand | — |
| D | Photosystem I reaction center subunit D | protein | 142 | 18% helix, 20% strand | — |
| E | Photosystem I reaction center subunit E | protein | 68 | 0% helix, 31% strand | — |
| F | Photosystem I reaction center subunit F | protein | 158 | 62% helix, 4% strand | — |
| H | Photosystem I reaction center subunit H | protein | 61 | 46% helix, 0% strand | — |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 83% helix, 0% strand | S4Z1D9 |
| J | Photosystem I reaction center subunit IX | protein | 42 | 69% helix, 2% strand | S4Z1E9 |
| K | Photosystem I reaction center subunit K | protein | 84 | 43% helix, 2% strand | — |
| L | Photosystem I reaction center subunit L | protein | 146 | 60% helix, 1% strand | — |
| 1 | Chlorophyll a-B binding protein LHCA1 | protein | 193 | 58% helix, 0% strand | — |
| 3 | Chlorophyll a-B binding protein LHCA3 | protein | 222 | 48% helix, 0% strand | — |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 197 | 48% helix, 1% strand | Q9LKC7 |
| 6 | Chlorophyll a-B binding protein LHCA6 | protein | 211 | 48% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 137 copies · chains A, B, J, 3, K, L, F, I, 1, H, 4, 6
- BCR · Beta-carotene · ligand · 25 copies · chains A, B, J, K, F, I, L, H, 3, 4, 6
- CHL · Chlorophyll B · ligand · 11 copies · chains 1, 4, 3, 6
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains 1, 3, 4, 6
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains A, B, 1, 4, 3, 6
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains B, C, F, J
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains F, J, 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 · 2 copies · chains 4, 6
- CL0 · Chlorophyll A isomer · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.82 | 0.83 | 90 | CL0, CLA |
| 2 | 1126 | 0.79 | 0.80 | 91 | DGD |
| 3 | 912 | 0.76 | 0.79 | 103 | CLA |
| 4 | 523 | 0.73 | 0.81 | 54 | empty |
| 5 | 108 | 0.72 | 0.94 | 28 | empty |
Interfaces
33 interfaces between chains.
- A–B · 3472 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 978 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 833 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7EWK · Barley photosystem I-LHCI-Lhca6 supercomplex · the same entry in another collection · chain A against A, 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 S4Z1K7
- Every structure of UniProt S4Z289
- Every structure of UniProt S4Z1D9
- Every structure of UniProt S4Z1E9
- Every structure of UniProt Q9LKC7
- Elsewhere: RCSB PDB 7EWK · PDBe 7EWK · UniProt S4Z1K7 · UniProt S4Z289 · UniProt S4Z1D9 · UniProt S4Z1E9 · UniProt Q9LKC7
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