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The structure of photosystem I tetramer from chroococcidiopsis ts-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium
Analyse The structure of photosystem I tetramer from chroococcidiopsis ts-821, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QCO
- Type
- protein
- Length
- 8,812 residues
- Chains
- 44
- 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
- A0A2S6VGM5, A0A2S6VGS2, A0A2S6VD54, A0A2S6VI21, A0A2S6VHU0, A0A2S6VDZ1, A0A2S6VDT4, V5JYA2, A0A2S6V467, V5JYE0, A0A2S6V6A8
- Ligands
- CLA, BCR, SF4, PQN, LHG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 12 distinct chains · 46% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, e, a | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 728 | 54% helix, 4% strand | A0A2S6VGM5 |
| B, G, g, b | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 734 | 56% helix, 1% strand | A0A2S6VGS2 |
| C, H, h, c | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 81 | 12% helix, 17% strand | A0A2S6VD54 |
| D, n | Photosystem I reaction center subunit II | protein | 137 | 14% helix, 17% strand | A0A2S6VI21 |
| V, W, v, w | Photosystem I reaction center subunit IV | protein | 61 | 5% helix, 34% strand | A0A2S6VHU0 |
| F, O, o, f | Photosystem I reaction center subunit III | protein | 141 | 43% helix, 1% strand | A0A2S6VDZ1 |
| I, P, p, i | Photosystem I reaction center subunit VIII | protein | 39 | 49% helix, 0% strand | A0A2S6VDT4 |
| J, Q, q, j | Photosystem I reaction center subunit IX | protein | 37 | 70% helix, 0% strand | V5JYA2 |
| K, R, r, k | Photosystem I reaction center subunit psak | protein | 65 | 51% helix, 0% strand | A0A2S6V467 |
| L, S, s, l | Photosystem I reaction center subunit XI | protein | 150 | 55% helix, 0% strand | V5JYE0 |
| M, T, t, m | Photosystem I reaction center subunit XII | protein | 31 | 61% helix, 0% strand | A0A2S6V6A8 |
| N, d | Photosystem I reaction center subunit II | protein | 135 | 10% helix, 21% strand | A0A2S6VI21 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 359 copies · chains A, B, F, J, K, L, G, M, I, S, E, O, Q, R, g, T, P, e, o, q, r, s, b, t, p, i, l, a, f, j, k, m
- BCR · Beta-carotene · ligand · 78 copies · chains A, K, B, F, J, I, L, E, R, Q, G, O, P, S, T, e, r, g, o, q, p, s, a, k, j, b, f, i, l, m
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, B, C, E, G, H, e, g, h, a, b, c
- PQN · Phylloquinone · ligand · 8 copies · chains A, B, E, G, e, g, a, b
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains A, e, a
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 | 1099 | 0.83 | 0.84 | 133 | CLA |
| 2 | 429 | 0.83 | 0.91 | 59 | SF4, PQN |
| 3 | 534 | 0.82 | 0.88 | 62 | SF4, PQN |
| 4 | 500 | 0.82 | 0.88 | 65 | SF4, PQN |
| 5 | 503 | 0.81 | 0.88 | 69 | PQN, SF4 |
Interfaces
114 interfaces between chains.
- e–g · 3314 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3221 Ų buried · 34 hydrogen bonds · protein-protein
- E–G · 2935 Ų buried · 25 hydrogen bonds · protein-protein
- a–b · 2926 Ų buried · 26 hydrogen bonds · protein-protein
- h–n · 1409 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7QCO · The structure of Photosystem I tetramer from Chroococcidiopsis TS-821, a thermophilic… · the same entry in another collection · chain B against B, 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 A0A2S6VGM5
- Every structure of UniProt A0A2S6VGS2
- Every structure of UniProt A0A2S6VD54
- Every structure of UniProt A0A2S6VI21
- Every structure of UniProt A0A2S6VHU0
- Every structure of UniProt A0A2S6VDZ1
- Every structure of UniProt A0A2S6VDT4
- Every structure of UniProt V5JYA2
- Every structure of UniProt A0A2S6V467
- Every structure of UniProt V5JYE0
- Every structure of UniProt A0A2S6V6A8
- Elsewhere: RCSB PDB 7QCO · PDBe 7QCO · UniProt A0A2S6VGM5 · UniProt A0A2S6VGS2 · UniProt A0A2S6VD54 · UniProt A0A2S6VI21 · UniProt A0A2S6VHU0 · UniProt A0A2S6VDZ1 · UniProt A0A2S6VDT4 · UniProt V5JYA2 · UniProt A0A2S6V467 · UniProt V5JYE0 · UniProt A0A2S6V6A8
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