Research workbench
The structure of the moss psi-lhci reveals the evolution of the lhci antenna
Analyse The structure of the moss psi-lhci reveals the evolution of the lhci antenna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KUX
- Type
- protein
- Length
- 3,259 residues
- Chains
- 17
- 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
- Q8MFA3, Q8MFA2, A9T399, A0A2K1IW94, A9TEM8, A9RW10, Q6YXQ2, A9REG3, A9SPD7, A0A2K1IN36, A9SJ10, A9TCU9, Q6YXR3, Q6YXM2, A0A2K1JLW2, A9S1E1, Q6YXK4
- Ligands
- CLA, BCR, CHL, LUT, LHG, LMG, SF4, PQN, CL0, DGD
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 17 distinct chains · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 59% helix, 4% strand | Q8MFA3 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 732 | 58% helix, 2% strand | Q8MFA2 |
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 192 | 47% helix, 2% strand | A9T399 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 203 | 51% helix, 2% strand | A0A2K1IW94 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 218 | 43% helix, 1% strand | A9TEM8 |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 203 | 45% helix, 1% strand | A9RW10 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 14% helix, 20% strand | Q6YXQ2 |
| D | Psad | protein | 142 | 15% helix, 25% strand | A9REG3 |
| E | Psae | protein | 63 | 5% helix, 37% strand | A9SPD7 |
| F | Psi-F | protein | 160 | 55% helix, 5% strand | A0A2K1IN36 |
| G | Psi-G | protein | 91 | 64% helix, 4% strand | A9SJ10 |
| H | Psah | protein | 87 | 39% helix, 1% strand | A9TCU9 |
| I | Photosystem I reaction center subunit VIII | protein | 34 | 71% helix, 0% strand | Q6YXR3 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 66% helix, 2% strand | Q6YXM2 |
| K | Psak | protein | 81 | 53% helix, 10% strand | A0A2K1JLW2 |
| L | Psi subunit V | protein | 160 | 46% helix, 6% strand | A9S1E1 |
| M | Photosystem I reaction center subunit XII | protein | 30 | 87% helix, 0% strand | Q6YXK4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 141 copies · chains A, B, F, J, 3, K, D, H, L, I, M, G, 1, 4, 2
- BCR · Beta-carotene · ligand · 26 copies · chains A, K, B, G, F, 1, 3, I, L, J, H, M
- CHL · Chlorophyll B · ligand · 14 copies · chains B, 1, 4, 2, 3
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 10 copies · chains 1, 2, 3, 4, F
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 7 copies · chains A, B, 1, 4, 2, 3
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 4 copies · chains A, 2, J, B, F
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, J, B, 1, G, 4, F
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 | 776 | 0.84 | 0.86 | 67 | CL0, CLA |
| 2 | 839 | 0.80 | 0.83 | 81 | DGD |
| 3 | 448 | 0.78 | 0.86 | 42 | CL0, CLA |
| 4 | 963 | 0.75 | 0.78 | 106 | CLA, LHG |
| 5 | 405 | 0.72 | 0.83 | 48 | empty |
Interfaces
39 interfaces between chains.
- A–B · 3536 Ų buried · 46 hydrogen bonds · protein-protein
- H–L · 2004 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1555 Ų buried · 22 hydrogen bonds · protein-protein
- B–G · 1297 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 1246 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7KUX · The Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna · the same entry in another collection · chain M against M, 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 Q8MFA3
- Every structure of UniProt Q8MFA2
- Every structure of UniProt A9T399
- Every structure of UniProt A0A2K1IW94
- Every structure of UniProt A9TEM8
- Every structure of UniProt A9RW10
- Every structure of UniProt Q6YXQ2
- Every structure of UniProt A9REG3
- Every structure of UniProt A9SPD7
- Every structure of UniProt A0A2K1IN36
- Every structure of UniProt A9SJ10
- Every structure of UniProt A9TCU9
- Every structure of UniProt Q6YXR3
- Every structure of UniProt Q6YXM2
- Every structure of UniProt A0A2K1JLW2
- Every structure of UniProt A9S1E1
- Every structure of UniProt Q6YXK4
- Elsewhere: RCSB PDB 7KUX · PDBe 7KUX · UniProt Q8MFA3 · UniProt Q8MFA2 · UniProt A9T399 · UniProt A0A2K1IW94 · UniProt A9TEM8 · UniProt A9RW10 · UniProt Q6YXQ2 · UniProt A9REG3 · UniProt A9SPD7 · UniProt A0A2K1IN36 · UniProt A9SJ10 · UniProt A9TCU9 · UniProt Q6YXR3 · UniProt Q6YXM2 · UniProt A0A2K1JLW2 · UniProt A9S1E1 · UniProt Q6YXK4
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