Research workbench
Structure of the green algal photosystem I supercomplex with light- harvesting complex I
Analyse Structure of the green algal photosystem I supercomplex with light- harvesting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JO6
- Type
- protein
- Length
- 3,899 residues
- Chains
- 19
- 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
- P12154, P09144, Q00914, Q39615, P12352, P12356, P14224, A8IFG7, P59777, P14225, A8IL32, Q7DM26, A8JF10, Q84Y02, Q75VY7, Q75VZ0, Q75VY8, Q75VY6
- Ligands
- CLA, BCR, CHL, LUT, LHG, SF4, PQN, CL0, DGD, LMG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 19 distinct chains · 53% 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 | 738 | 62% helix, 5% strand | P12154 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 732 | 61% helix, 3% strand | P09144 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 14% helix, 20% strand | Q00914 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 144 | 13% helix, 21% strand | Q39615 |
| E | Photosystem I reaction center subunit IV, chloroplastic | protein | 61 | 0% helix, 36% strand | P12352 |
| F | Photosystem I reaction center subunit F, photosystem I reaction center subunit III, chloroplastic | protein | 165 | 64% helix, 5% strand | P12356 |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 68 | 71% helix, 0% strand | P14224 |
| I | Photosystem I reaction center subunit VIII | protein | 37 | 68% helix, 3% strand | A8IFG7 |
| J | Photosystem I reaction center subunit IX | protein | 39 | 74% helix, 3% strand | P59777 |
| K | Photosystem I reaction center subunit psak, chloroplastic | protein | 45 | 80% helix, 0% strand | P14225 |
| L | Photosystem I reaction center subunit XI | protein | 118 | 70% helix, 0% strand | A8IL32 |
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 194 | 50% helix, 3% strand | Q7DM26 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 202 | 51% helix, 1% strand | A8JF10 |
| 7 | Chlorophyll a-B binding protein, chloroplastic | protein | 212 | 52% helix, 1% strand | Q84Y02 |
| 8 | Chlorophyll a-B binding protein, chloroplastic | protein | 217 | 50% helix, 0% strand | Q75VY7 |
| Z | Chlorophyll a-B binding protein, chloroplastic | protein | 192 | 49% helix, 3% strand | Q7DM26 |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 203 | 52% helix, 1% strand | Q75VZ0 |
| 5 | Chlorophyll a-B binding protein, chloroplastic | protein | 223 | 47% helix, 3% strand | Q75VY8 |
| 6 | Chlorophyll a-B binding protein, chloroplastic | protein | 229 | 44% helix, 4% strand | Q75VY6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 197 copies · chains A, B, F, J, 3, 7, K, L, D, I, G, 1, 8, Z, 5, 6, 4
- BCR · Beta-carotene · ligand · 32 copies · chains A, B, J, F, G, I, K, L, 3, 5, 7, 8, 4, 6
- CHL · Chlorophyll B · ligand · 18 copies · chains 1, 8, 3, 7, Z, 4, 5, 6
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 18 copies · chains 1, G, 3, 7, 8, Z, 4, 5, 6
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, 3, B, 1, 8, 7, Z, 4, 6, 5
- 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, D
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains F, J
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 | 1059 | 0.82 | 0.83 | 86 | CLA, DGD |
| 2 | 389 | 0.77 | 0.86 | 47 | CL0, CLA |
| 3 | 767 | 0.72 | 0.77 | 103 | CLA |
| 4 | 693 | 0.71 | 0.77 | 61 | CLA |
| 5 | 113 | 0.71 | 0.92 | 33 | SF4, PQN |
Interfaces
38 interfaces between chains.
- A–B · 3506 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1622 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1114 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1084 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1017 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JO6 · Structure of the green algal photosystem I supercomplex with light-harvesting complex I · the same entry in another collection · chain L against L, 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 P12154
- Every structure of UniProt P09144
- Every structure of UniProt Q00914
- Every structure of UniProt Q39615
- Every structure of UniProt P12352
- Every structure of UniProt P12356
- Every structure of UniProt P14224
- Every structure of UniProt A8IFG7
- Every structure of UniProt P59777
- Every structure of UniProt P14225
- Every structure of UniProt A8IL32
- Every structure of UniProt Q7DM26
- Every structure of UniProt A8JF10
- Every structure of UniProt Q84Y02
- Every structure of UniProt Q75VY7
- Every structure of UniProt Q75VZ0
- Every structure of UniProt Q75VY8
- Every structure of UniProt Q75VY6
- Elsewhere: RCSB PDB 6JO6 · PDBe 6JO6 · UniProt P12154 · UniProt P09144 · UniProt Q00914 · UniProt Q39615 · UniProt P12352 · UniProt P12356 · UniProt P14224 · UniProt A8IFG7 · UniProt P59777 · UniProt P14225 · UniProt A8IL32 · UniProt Q7DM26 · UniProt A8JF10 · UniProt Q84Y02 · UniProt Q75VY7 · UniProt Q75VZ0 · UniProt Q75VY8 · UniProt Q75VY6
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