Research workbench
Photosystem I tetramer
Analyse Photosystem I tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCL
- Type
- protein
- Length
- 9,058 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Nostoc sp. PCC 7120
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- P58576, P58565, P0A410, P58573, P58575, P58564, P58560, P58568, P58583, P58577, Q8YNB0, P58566
- Ligands
- CLA, BCR, LMG, LHG, AJP, SF4, PQN, CL0, ECH, DGD
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 3.2 · 19 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A1, A2, A, AA | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 740 | 61% helix, 5% strand | P58576 |
| B1, B2, B, BB | Photosystem I P700 chlorophyll a apoprotein A2 1 (EC 1.97.1.12) | protein | 739 | 60% helix, 3% strand | P58565 |
| C1, C2, C, CC | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 14% helix, 19% strand | P0A410 |
| D1, D2, D, DD | Photosystem I reaction center subunit II | protein | 134 | 18% helix, 23% strand | P58573 |
| E1, E2 | Photosystem I reaction center subunit IV | protein | 60 | 0% helix, 33% strand | P58575 |
| F1, F, FF | Photosystem I reaction center subunit III | protein | 139 | 53% helix, 5% strand | P58564 |
| I1, I, II | Photosystem I reaction center subunit VIII | protein | 31 | 84% helix, 0% strand | P58560 |
| J1, J2, J, JJ | Photosystem I reaction center subunit IX | protein | 43 | 72% helix, 0% strand | P58568 |
| K1 | Photosystem I reaction center subunit PsaK 1 | protein | 74 | 58% helix, 0% strand | P58583 |
| L1 | Photosystem I reaction center subunit XI | protein | 166 | 53% helix, 3% strand | P58577 |
| M1, M2, M, MM | Photosystem I reaction center subunit XII | protein | 31 | 84% helix, 0% strand | Q8YNB0 |
| X1, X2, X, XX | Photosystem I 4.8 kDa protein | protein | 39 | 54% helix, 0% strand | P58566 |
| F2 | Photosystem I reaction center subunit III | protein | 137 | 47% helix, 5% strand | P58564 |
| I2 | Photosystem I reaction center subunit VIII | protein | 33 | 79% helix, 0% strand | P58560 |
| K2 | Photosystem I reaction center subunit PsaK 1 | protein | 73 | 56% helix, 0% strand | P58583 |
| L2 | Photosystem I reaction center subunit XI | protein | 167 | 54% helix, 3% strand | P58577 |
| E, EE | Photosystem I reaction center subunit IV | protein | 63 | 0% helix, 37% strand | P58575 |
| K, KK | Photosystem I reaction center subunit PsaK 1 | protein | 60 | 68% helix, 0% strand | P58583 |
| L, LL | Photosystem I reaction center subunit XI | protein | 154 | 60% helix, 3% strand | P58577 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 378 copies · chains A1, B1, F1, J1, K1, L1, I1, BB, M1, L, X1, A2, B2, K2, F2, J2, L2, I2, B, M2, LL, X2, A, F, J, K, I, M, X, AA, FF, JJ, KK, II, MM, XX
- BCR · Beta-carotene · ligand · 94 copies · chains A1, B1, F1, J1, I1, K1, L1, M1, A2, B2, F2, J2, I2, L2, K2, M2, A, B, K, F, J, I, L, M, AA, BB, KK, FF, JJ, II, LL, MM
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 30 copies · chains A1, L1, B1, L, I1, M1, K1, BB, A2, L2, B2, LL, I2, M2, K2, B, M, I, II, MM
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 24 copies · chains A1, B1, X1, I1, L1, L, A2, B2, X2, I2, L2, LL, A, B, X, F, AA, BB, XX, FF
- AJP · Digitonin · ligand · 22 copies · chains A1, L1, BB, A2, I2, M2, LL, L2, B, AA, A, K2, I, L, K, I1, M1, K1, II, KK
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A1, B1, C1, A2, B2, C2, A, B, C, AA, BB, CC
- PQN · Phylloquinone · ligand · 8 copies · chains A1, J1, B1, A2, J2, B2, A, J, B, AA, JJ, BB
- CL0 · Chlorophyll A isomer · ligand · 4 copies · chains A1, B1, A2, B2, A, B, AA, BB
- ECH · beta,beta-caroten-4-one · ligand · 4 copies · chains B1, B2, B, BB
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · 2 copies · chains A2, B, A1, BB
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 | 949 | 0.78 | 0.80 | 70 | CLA, LMG |
| 2 | 1170 | 0.78 | 0.80 | 87 | CLA, LMG |
| 3 | 725 | 0.77 | 0.82 | 65 | LMG |
| 4 | 668 | 0.76 | 0.81 | 58 | LMG |
| 5 | 325 | 0.76 | 0.86 | 39 | CLA |
Interfaces
122 interfaces between chains.
- A–B · 3597 Ų buried · 41 hydrogen bonds · protein-protein
- A1–B1 · 3596 Ų buried · 37 hydrogen bonds · protein-protein
- AA–BB · 3581 Ų buried · 36 hydrogen bonds · protein-protein
- A2–B2 · 3522 Ų buried · 35 hydrogen bonds · protein-protein
- C1–D1 · 1737 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- P58576 · AlphaFold monomer V2.0 prediction for photosystem I P700 chlorophyll a apoprotein A1… · a predicted model of the same protein · chain A1 against A, TM-score 1.00
- P58565 · AlphaFold monomer V2.0 prediction for photosystem I P700 chlorophyll a apoprotein A2 1… · a predicted model of the same protein · chain B1 against A, TM-score 1.00
- P58564 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit III (P58564) · a predicted model of the same protein · chain F1 against A, TM-score 0.97
- P58573 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit II (P58573) · a predicted model of the same protein · chain D1 against A, TM-score 0.97
- P58575 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit IV (P58575) · a predicted model of the same protein · chain E1 against A, TM-score 0.96
- P0A410 · AlphaFold monomer V2.0 prediction for photosystem I iron-sulfur center (P0A410) · a predicted model of the same protein · chain C1 against A, TM-score 0.93
- P58583 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit psak 1… · a predicted model of the same protein · chain K1 against A, TM-score 0.92
- P58577 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit XI (P58577) · a predicted model of the same protein · chain L against A, TM-score 0.90
- P58560 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit VIII (P58560) · a predicted model of the same protein · chain I1 against A, TM-score 0.88
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 P58576
- Every structure of UniProt P58565
- Every structure of UniProt P0A410
- Every structure of UniProt P58573
- Every structure of UniProt P58575
- Every structure of UniProt P58564
- Every structure of UniProt P58560
- Every structure of UniProt P58568
- Every structure of UniProt P58583
- Every structure of UniProt P58577
- Every structure of UniProt Q8YNB0
- Every structure of UniProt P58566
- Elsewhere: RCSB PDB 6TCL · PDBe 6TCL · UniProt P58576 · UniProt P58565 · UniProt P0A410 · UniProt P58573 · UniProt P58575 · UniProt P58564 · UniProt P58560 · UniProt P58568 · UniProt P58583 · UniProt P58577 · UniProt Q8YNB0 · UniProt P58566
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