MolNFT v1 · #152503 · protein
Photosystem I of chlamydomonas reinhardtii
6IJO · Psaa: “Photosystem I of chlamydomonas reinhardtii”. Electron microscopy, 11 ligands (CLA, BCR, LHG), 20 pockets (best druggability 0.82). MolNFT v1 #152503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IJO
- Type
- protein
- Length
- 4,382 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Psaa; Psab; Psac; Psad; Psae; Psaf; Psag; Psah; Psai; Psaj; Psak; Psal; LHCA1; LHCA3…
- Ligands
- CLA, BCR, LHG, LUT, XAT, LMU, LMG, SF4, PQN, DGD, NEX
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 23 distinct chains · 49% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Psaa | protein | 741 | 59% helix, 3% strand | — |
| B | Psab | protein | 731 | 59% helix, 2% strand | — |
| C | Psac | protein | 80 | 6% helix, 16% strand | — |
| D | Psad | protein | 144 | 13% helix, 22% strand | — |
| E | Psae | protein | 64 | 0% helix, 34% strand | — |
| F | Psaf | protein | 164 | 52% helix, 4% strand | — |
| G | Psag | protein | 70 | 54% helix, 0% strand | — |
| H | Psah | protein | 51 | 37% helix, 0% strand | — |
| I | Psai | protein | 32 | 69% helix, 0% strand | — |
| J | Psaj | protein | 41 | 68% helix, 0% strand | — |
| K | Psak | protein | 85 | 51% helix, 7% strand | — |
| L | Psal | protein | 106 | 63% helix, 0% strand | — |
| 1 | LHCA1 | protein | 193 | 46% helix, 2% strand | — |
| a | LHCA1 | protein | 194 | 45% helix, 2% strand | — |
| 3 | LHCA3 | protein | 221 | 50% helix, 0% strand | — |
| 4 | LHCA4 | protein | 210 | 50% helix, 1% strand | — |
| 5 | LHCA5 | protein | 226 | 42% helix, 2% strand | — |
| 6 | LHCA6 | protein | 230 | 40% helix, 6% strand | — |
| 7 | LHCA7 | protein | 213 | 50% helix, 1% strand | — |
| 8 | LHCA8 | protein | 215 | 47% helix, 0% strand | — |
| 2 | LHCA2 | protein | 173 | 49% helix, 0% strand | — |
| 9 | LHCA9 | protein | 172 | 42% helix, 0% strand | — |
| X | Chainx | protein | 26 | 88% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 243 copies · chains A, B, F, J, 3, K, D, L, I, H, 9, G, 1, 8, a, 4, 7, 5, 6, 2, X
- BCR · Beta-carotene · ligand · 31 copies · chains A, B, J, F, G, 9, K, I, L, 1, a, 3, 5, 4, 6, 7, 8
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 16 copies · chains A, B, 1, 8, a, 4, 3, 5, 7, 6, 2, 9
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 10 copies · chains 1, a, 3, 4, 5, 6, 7, 8, 2, 9
- 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 · 10 copies · chains 1, a, 3, 4, 5, 6, 7, 8, 2, 9
- LMU · Dodecyl-alpha-D-maltoside · ligand · 7 copies · chains A, 3, L, K, 5, 6, 8, 4
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 7 copies · chains A, J, 7, F, 4, 6, 8, 3, 5
- 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, D, F, J, 8
- 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 · 2 copies · chains 5, 6, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.82 | 0.86 | 66 | CLA |
| 2 | 1185 | 0.81 | 0.82 | 109 | CLA, DGD |
| 3 | 1019 | 0.74 | 0.77 | 127 | CLA |
| 4 | 936 | 0.72 | 0.76 | 96 | CLA |
| 5 | 398 | 0.72 | 0.83 | 43 | empty |
Interfaces
50 interfaces between chains.
- A–B · 3525 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1665 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1163 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1123 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1025 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6IJO · Photosystem I of Chlamydomonas reinhardtii · 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
- Elsewhere: RCSB PDB 6IJO · PDBe 6IJO
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