MolNFT v1 · #152498 · protein
Photosystem I of chlamydomonas reinhardtii
6IJJ · Psaa: “Photosystem I of chlamydomonas reinhardtii”. Electron microscopy, 11 ligands (CLA, BCR, LHG), 20 pockets (best druggability 0.85). MolNFT v1 #152498 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IJJ
- Type
- protein
- Length
- 3,889 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Psaa; Psab; Psac; Psad; Psae; Psaf; Psai; Psaj; Psak; Psal; LHCA1; LHCA3; LHCA4; LHCA5…
- Ligands
- CLA, BCR, LHG, LUT, XAT, LMU, LMG, SF4, PQN, DGD, NEX
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 18 distinct chains · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Psaa | protein | 741 | 60% helix, 4% strand | — |
| B | Psab | protein | 731 | 59% helix, 2% strand | — |
| C | Psac | protein | 80 | 11% helix, 21% strand | — |
| D | Psad | protein | 144 | 15% helix, 24% strand | — |
| E | Psae | protein | 64 | 0% helix, 34% strand | — |
| F | Psaf | protein | 164 | 52% helix, 5% strand | — |
| I | Psai | protein | 32 | 59% helix, 0% strand | — |
| J | Psaj | protein | 41 | 71% helix, 2% strand | — |
| K | Psak | protein | 85 | 48% helix, 8% strand | — |
| L | Psal | protein | 105 | 73% helix, 0% strand | — |
| 1 | LHCA1 | protein | 193 | 46% helix, 3% strand | — |
| a | LHCA1 | protein | 194 | 46% helix, 3% strand | — |
| 3 | LHCA3 | protein | 221 | 52% helix, 0% strand | — |
| 4 | LHCA4 | protein | 210 | 51% helix, 1% strand | — |
| 5 | LHCA5 | protein | 226 | 46% helix, 3% strand | — |
| 6 | LHCA6 | protein | 230 | 42% helix, 6% strand | — |
| 7 | LHCA7 | protein | 213 | 51% helix, 1% strand | — |
| 8 | LHCA8 | protein | 215 | 51% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 216 copies · chains A, B, F, J, 3, 7, K, D, L, I, 1, 8, a, 4, 5, 6
- BCR · Beta-carotene · ligand · 30 copies · chains A, B, J, F, K, I, L, 1, a, 3, 5, 4, 6, 7, 8
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains A, B, 1, 8, a, 4, 3, 5, 7, 6
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 8 copies · chains 1, a, 3, 4, 5, 6, 7, 8
- 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 · 8 copies · chains 1, a, 3, 4, 5, 6, 7, 8
- 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
- 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
- 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 | 872 | 0.85 | 0.86 | 85 | CLA |
| 2 | 1181 | 0.81 | 0.82 | 101 | CLA, DGD |
| 3 | 401 | 0.72 | 0.83 | 49 | empty |
| 4 | 61 | 0.71 | 0.97 | 20 | SF4 |
| 5 | 665 | 0.70 | 0.77 | 66 | CLA |
Interfaces
38 interfaces between chains.
- A–B · 3523 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1646 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1155 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1116 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 987 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6IJJ · Photosystem I of Chlamydomonas reinhardtii · 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
- Elsewhere: RCSB PDB 6IJJ · PDBe 6IJJ
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