Research workbench
Barley photosystem I-lhci-LHCA5 supercomplex
Analyse Barley photosystem I-lhci-LHCA5 supercomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EW6
- Type
- protein
- Length
- 3,108 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, S4YZ47, P36213, P13194, P13192, P20143, S4Z1D9, S4Z1E9, P36886, P23993, A0A287WC32, Q43485, F2DAN8
- Ligands
- CLA, BCR, CHL, LUT, LHG, LMG, SF4, PQN, DGD, XAT, CL0
- Pockets
- 20 · best druggability 0.78
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 (EC 1.97.1.12) | protein | 81 | 11% helix, 20% strand | S4YZ47 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 142 | 16% helix, 18% strand | P36213 |
| E | Photosystem I reaction center subunit IV, chloroplastic | protein | 68 | 4% helix, 28% strand | P13194 |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 158 | 54% helix, 5% strand | P13192 |
| H | Photosystem I reaction center subunit VI, chloroplastic | protein | 61 | 52% helix, 0% strand | P20143 |
| 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 psak, chloroplastic | protein | 84 | 44% helix, 2% strand | P36886 |
| L | Photosystem I reaction center subunit XI, chloroplastic | protein | 146 | 60% helix, 1% strand | P23993 |
| 1 | Chlorophyll a-B binding protein LHCA1 | protein | 191 | 54% helix, 1% strand | A0A287WC32 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 203 | 49% helix, 0% strand | Q43485 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 222 | 50% helix, 0% strand | F2DAN8 |
| 5 | Chlorophyll a-B binding protein LHCA5 | protein | 205 | 51% helix, 1% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 136 copies · chains A, B, F, J, K, L, I, H, 1, 3, 5, 2
- BCR · Beta-carotene · ligand · 25 copies · chains A, B, J, K, L, F, I, H, 1, 2, 3, 5
- CHL · Chlorophyll B · ligand · 12 copies · chains 1, 5, 2, 3
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains 1, 2, 3, 5
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains A, B, 1, 5, 2, 3
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 5 copies · chains F, J, 5, 2, 1
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains B, C, F, J
- 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 2, F, 5
- 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 | 1103 | 0.78 | 0.80 | 84 | CLA, DGD |
| 2 | 926 | 0.75 | 0.78 | 80 | empty |
| 3 | 265 | 0.73 | 0.86 | 38 | CLA |
| 4 | 1049 | 0.73 | 0.76 | 106 | CLA |
| 5 | 72 | 0.73 | 0.97 | 20 | empty |
Interfaces
33 interfaces between chains.
- A–B · 3424 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1624 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 937 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 892 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 869 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EW6 · Barley photosystem I-LHCI-Lhca5 supercomplex · the same entry in another collection · chain 5 against 5, 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 S4YZ47
- Every structure of UniProt P36213
- Every structure of UniProt P13194
- Every structure of UniProt P13192
- Every structure of UniProt P20143
- Every structure of UniProt S4Z1D9
- Every structure of UniProt S4Z1E9
- Every structure of UniProt P36886
- Every structure of UniProt P23993
- Every structure of UniProt A0A287WC32
- Every structure of UniProt Q43485
- Every structure of UniProt F2DAN8
- Elsewhere: RCSB PDB 7EW6 · PDBe 7EW6 · UniProt S4Z1K7 · UniProt S4Z289 · UniProt S4YZ47 · UniProt P36213 · UniProt P13194 · UniProt P13192 · UniProt P20143 · UniProt S4Z1D9 · UniProt S4Z1E9 · UniProt P36886 · UniProt P23993 · UniProt A0A287WC32 · UniProt Q43485 · UniProt F2DAN8
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