Research workbench
Dunaliella photosystem I supercomplex
Analyse Dunaliella photosystem I supercomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SL5
- Type
- protein
- Length
- 3,744 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
- D0FXV2, D0FXZ0, D0FXW7, D0FXW0, C1K003
- Ligands
- CLA, BCR, LHG, CHL, PTY, LUT, LMG, XAT, LMU, DGD, 3PH, SF4, SQD, PQN, 4RF, LMK…
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 19 distinct chains · 51% 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 | 740 | 58% helix, 4% strand | D0FXV2 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 58% helix, 2% strand | D0FXZ0 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 15% helix, 21% strand | D0FXW7 |
| D | Psad | protein | 143 | 13% helix, 24% strand | — |
| E | Psae | protein | 64 | 0% helix, 34% strand | — |
| F | Psaf | protein | 162 | 53% helix, 4% strand | — |
| J | Photosystem I reaction center subunit IX | protein | 41 | 66% helix, 0% strand | D0FXW0 |
| G | Psag | protein | 101 | 46% helix, 0% strand | — |
| H | Psah | protein | 92 | 34% helix, 0% strand | — |
| I | Psai | protein | 39 | 62% helix, 0% strand | — |
| K | Psak | protein | 84 | 50% helix, 5% strand | — |
| L | Psal | protein | 155 | 57% helix, 1% strand | — |
| O | Psao | protein | 86 | 56% helix, 0% strand | — |
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 197 | 53% helix, 0% strand | C1K003 |
| 2 | LHCA2 | protein | 208 | 49% helix, 0% strand | — |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 228 | 48% helix, 0% strand | — |
| 4 | LHCA4 | protein | 211 | 46% helix, 1% strand | — |
| 5 | LHCA5 | protein | 202 | 54% helix, 1% strand | — |
| 6 | LHCA6 | protein | 178 | 55% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 172 copies · chains A, B, F, J, 3, K, O, L, H, I, G, 6, 1, 5, 4, 2
- BCR · Beta-carotene · ligand · 31 copies · chains A, K, O, B, G, 6, F, J, H, L, I, 1, 2, 3, 4
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 15 copies · chains A, B, 1, F, 4, G, 2, 3, J, 5, 6
- CHL · Chlorophyll B · ligand · 13 copies · chains 1, 4, G, 2, 3, 5, 6, B
- PTY · Phosphatidylethanolamine · ligand · 9 copies · chains L, K, O, F, J, 1, A, 2, 3, 4, H, I, 5, B
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 9 copies · chains 1, 2, 3, 4, 5, B, 6
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 8 copies · chains F, J, G, 1, 2, 4, A, 3, B, 5, 6
- 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 · 6 copies · chains 1, 2, 3, 4, 6
- LMU · Dodecyl-alpha-D-maltoside · ligand · 4 copies · chains A, J, B, 6
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 4 copies · chains B, C, 2, 4, 3, A
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 4 copies · chains B, I, F, 5
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 3 copies · chains F, 2, A, 3, 6
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- 4RF · Tripalmitoylglycerol · ligand · 2 copies · chains A, L, H, I, 5
- LMK · trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium · ligand · 2 copies · chains J, 4
- P3H · [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R}, 6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5, 8-dienoate · ligand · 2 copies · chains A, 2, B, I, 5
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- OCD · octadecanal · ligand · chains A
- CA · Calcium ion · metal · chains 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 | 1043 | 0.83 | 0.84 | 113 | empty |
| 2 | 732 | 0.77 | 0.81 | 62 | DGD |
| 3 | 700 | 0.70 | 0.77 | 66 | CLA |
| 4 | 401 | 0.69 | 0.81 | 47 | empty |
| 5 | 212 | 0.69 | 0.85 | 26 | CLA |
Interfaces
48 interfaces between chains.
- A–B · 3598 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1989 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1602 Ų buried · 27 hydrogen bonds · protein-protein
- B–G · 1499 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1167 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6SL5 · Dunaliella Photosystem I Supercomplex · 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
- Every structure of UniProt D0FXV2
- Every structure of UniProt D0FXZ0
- Every structure of UniProt D0FXW7
- Every structure of UniProt D0FXW0
- Every structure of UniProt C1K003
- Elsewhere: RCSB PDB 6SL5 · PDBe 6SL5 · UniProt D0FXV2 · UniProt D0FXZ0 · UniProt D0FXW7 · UniProt D0FXW0 · UniProt C1K003
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