Research workbench
Structure of a minimal photosystem I
Analyse Structure of a minimal photosystem I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O1V
- Type
- protein
- Length
- 1,869 residues
- Chains
- 7
- 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
- P29254, P29255, P32422, P19569, P12975, P74564, P72986
- Ligands
- CLA, BCR, LHG, LMG, SF4, PQN, ECH, SQD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 739 | 58% helix, 4% strand | P29254 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 729 | 59% helix, 1% strand | P29255 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 20% helix, 20% strand | P32422 |
| D | Photosystem I reaction center subunit II | protein | 141 | 16% helix, 23% strand | P19569 |
| E | Photosystem I reaction center subunit IV | protein | 69 | 4% helix, 32% strand | P12975 |
| K | Photosystem I reaction center subunit psak 2 | protein | 80 | 48% helix, 0% strand | P74564 |
| M | Photosystem I reaction center subunit XII | protein | 31 | 77% helix, 0% strand | P72986 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 88 copies · chains A, B, K, M
- BCR · Beta-carotene · ligand · 15 copies · chains A, K, B
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains A, E, B, M
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 4 copies · chains A, B, K
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- ECH · beta,beta-caroten-4-one · ligand · 2 copies · chains B, M
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 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 | 1031 | 0.83 | 0.83 | 88 | CLA |
| 2 | 754 | 0.80 | 0.83 | 63 | LMG |
| 3 | 74 | 0.73 | 0.97 | 22 | empty |
| 4 | 681 | 0.70 | 0.77 | 64 | CLA |
| 5 | 438 | 0.68 | 0.79 | 44 | CLA |
Interfaces
12 interfaces between chains.
- A–B · 3502 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1509 Ų buried · 18 hydrogen bonds · protein-protein
- B–M · 991 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 917 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 810 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7O1V · Structure of a Minimal Photosystem I · the same entry in another collection · chain M against M, TM-score 1.00
- P29254 · AlphaFold monomer V2.0 prediction for photosystem I P700 chlorophyll a apoprotein A1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P29255 · AlphaFold monomer V2.0 prediction for photosystem I P700 chlorophyll a apoprotein A2… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P32422 · AlphaFold monomer V2.0 prediction for photosystem I iron-sulfur center (P32422) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P19569 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit II (P19569) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P12975 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit IV (P12975) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 P29254
- Every structure of UniProt P29255
- Every structure of UniProt P32422
- Every structure of UniProt P19569
- Every structure of UniProt P12975
- Every structure of UniProt P74564
- Every structure of UniProt P72986
- Elsewhere: RCSB PDB 7O1V · PDBe 7O1V · UniProt P29254 · UniProt P29255 · UniProt P32422 · UniProt P19569 · UniProt P12975 · UniProt P74564 · UniProt P72986
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