Research workbench
The structure of a red shifted photosystem I complex
Analyse The structure of a red shifted photosystem I complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UZV
- Type
- protein
- Length
- 6,711 residues
- Chains
- 33
- 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, P32422, P19569, P12975, P29256, Q55330, Q55329, P37277, P72986, P74564
- Ligands
- CLA, BCR, LHG, LMG, SF4, PQN, CL0, CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a, 1 | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 739 | 58% helix, 4% strand | P29254 |
| B, b, 2 | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 733 | 57% helix, 3% strand | — |
| C, c, 3 | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 11% helix, 20% strand | P32422 |
| D, d, 4 | Photosystem I reaction center subunit II | protein | 138 | 14% helix, 22% strand | P19569 |
| E, e, 5 | Photosystem I reaction center subunit IV | protein | 68 | 0% helix, 34% strand | P12975 |
| F, f, 6 | Photosystem I reaction center subunit III | protein | 141 | 55% helix, 6% strand | P29256 |
| I, i, h | Photosystem I reaction center subunit VIII | protein | 37 | 70% helix, 0% strand | Q55330 |
| J, j, 7 | Photosystem I reaction center subunit IX | protein | 39 | 72% helix, 3% strand | Q55329 |
| L, l, 0 | Photosystem I reaction center subunit XI | protein | 153 | 62% helix, 4% strand | P37277 |
| M, m, 9 | Photosystem I reaction center subunit XII | protein | 30 | 87% helix, 0% strand | P72986 |
| K, k, 8 | Photosystem I reaction center subunit psak 2 | protein | 79 | 65% helix, 0% strand | P74564 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 288 copies · chains A, B, F, J, K, L, I, 0, b, m, D, M, 8, i, l, a, f, j, k, 2, 9, 1, 7, h, 6, d, 4
- BCR · Beta-carotene · ligand · 69 copies · chains A, B, F, J, I, L, l, M, K, a, b, 1, 2, f, j, m, 6, 7, i, h, 0, k, 8, 9
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, E, B, I, M, 0, a, e, 1, 5, b, 2, L, i, m, h, l, 9
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, L, m, B, i, l, a, 9, M, 1, b, 2, h, I, 0
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, a, b, 1, 2, c, 3
- PQN · Phylloquinone · ligand · 6 copies · chains A, B, a, 1, b, 2
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains A, B, a, b, 1, 2
- CA · Calcium ion · metal · 3 copies · chains A, L, 0, a, l, 1
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, F, I, 0, a, f, 1, 6, 7, L, i, h, l
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 | 1198 | 0.86 | 0.86 | 107 | CL0, CLA |
| 2 | 1016 | 0.86 | 0.86 | 98 | CL0, CLA |
| 3 | 1059 | 0.86 | 0.86 | 106 | CL0, CLA |
| 4 | 1057 | 0.84 | 0.84 | 100 | CLA, BCR |
| 5 | 1180 | 0.79 | 0.80 | 94 | LMG, CLA |
Interfaces
90 interfaces between chains.
- A–B · 3553 Ų buried · 38 hydrogen bonds · protein-protein
- a–b · 3553 Ų buried · 42 hydrogen bonds · protein-protein
- 1–2 · 3531 Ų buried · 37 hydrogen bonds · protein-protein
- c–d · 1612 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 1611 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6UZV · The structure of a red shifted photosystem I complex · the same entry in another collection · chain K against K, 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 P29254
- Every structure of UniProt P32422
- Every structure of UniProt P19569
- Every structure of UniProt P12975
- Every structure of UniProt P29256
- Every structure of UniProt Q55330
- Every structure of UniProt Q55329
- Every structure of UniProt P37277
- Every structure of UniProt P72986
- Every structure of UniProt P74564
- Elsewhere: RCSB PDB 6UZV · PDBe 6UZV · UniProt P29254 · UniProt P32422 · UniProt P19569 · UniProt P12975 · UniProt P29256 · UniProt Q55330 · UniProt Q55329 · UniProt P37277 · UniProt P72986 · UniProt P74564
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