Research workbench
Dimeric PSI of Chlamydomonas reinhardtii at 2.74 A resolution (symmetry expanded)
Analyse Dimeric PSI of Chlamydomonas reinhardtii at 2.74 A resolution (symmetry… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZQ9
- Type
- protein
- Length
- 4,713 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.74
- Source
- Chlamydomonas reinhardtii
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- P12154, P09144, Q00914, Q39615, P12352, P12356, P14224, A8IFG7, P59777, A8IL32, P14225, Q05093, A8JF10, Q84Y02, Q75VY7, Q75VZ0, Q75VY8, Q75VY6, A8ITV3
- Ligands
- CLA, BCR, CHL, LUT, LMG, LHG, XAT, SF4, PQN, NEX, CL0, LMU, DGD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.74 · 22 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 63% helix, 5% strand | P12154 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 63% helix, 3% strand | P09144 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | Q00914 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 144 | 17% helix, 25% strand | Q39615 |
| E | Photosystem I reaction center subunit IV, chloroplastic | protein | 64 | 5% helix, 36% strand | P12352 |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 165 | 66% helix, 5% strand | P12356 |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 95 | 62% helix, 0% strand | P14224 |
| I, I2 | Photosystem I reaction center subunit VIII | protein | 37 | 70% helix, 3% strand | A8IFG7 |
| J | Photosystem I reaction center subunit IX | protein | 40 | 73% helix, 3% strand | P59777 |
| L | PSI subunit V | protein | 124 | 69% helix, 1% strand | A8IL32 |
| K | Photosystem I reaction center subunit psaK, chloroplastic | protein | 86 | 50% helix, 9% strand | P14225 |
| 1, Z | Chlorophyll a-b binding protein, chloroplastic | protein | 194 | 53% helix, 2% strand | Q05093 |
| 3 | Chlorophyll a-b binding protein, chloroplastic | protein | 227 | 52% helix, 1% strand | A8JF10 |
| 7 | Chlorophyll a-b binding protein, chloroplastic | protein | 213 | 56% helix, 1% strand | Q84Y02 |
| 8 | Chlorophyll a-b binding protein, chloroplastic | protein | 217 | 61% helix, 0% strand | Q75VY7 |
| 4 | Chlorophyll a-b binding protein, chloroplastic (Lhca4) | protein | 212 | 52% helix, 2% strand | Q75VZ0 |
| 5 | Chlorophyll a-b binding protein, chloroplastic | protein | 227 | 50% helix, 5% strand | Q75VY8 |
| 6 | Chlorophyll a-b binding protein, chloroplastic | protein | 230 | 48% helix, 8% strand | Q75VY6 |
| 9 | Chlorophyll a-b binding protein, chloroplastic | protein | 186 | 57% helix, 1% strand | A8ITV3 |
| B2 | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 180 | 51% helix, 3% strand | — |
| L2 | PSI subunit V | protein | 102 | 73% helix, 0% strand | A8IL32 |
| 92 | Chlorophyll a-b binding protein, chloroplastic | protein | 184 | 58% helix, 1% strand | A8ITV3 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 226 copies · chains A, B, F, J, 3, K, 7, L, D, I, G, 9, 1, 8, Z, 5, 6, 4, I2, L2, B2, 92
- BCR · Beta-carotene · ligand · 36 copies · chains A, B, G, F, J, 9, I, L, K, 3, 5, 7, 8, 4, 6, I2, B2, 92, L2
- CHL · Chlorophyll B · ligand · 32 copies · chains 1, 8, 3, 7, Z, 4, 6, 5, 9, B, 92, B2
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 20 copies · chains A, J, F, 1, G, 3, 7, 8, 4, Z, 5, 6, 9, 92
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 17 copies · chains A, L, J, 7, B, I, G, F, 1, 8, 3, 5, 4, 6, 9, B2, I2, 92
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 16 copies · chains A, B, 1, 8, 3, 7, 5, Z, 4, 6, 9, 92
- 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 · 7 copies · chains 1, 7, 8, Z, 4, 5, 6
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 2 copies · chains 5, 6, 4
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- LMU · Dodecyl-alpha-D-maltoside · sugar · 34 copies · chains A, 3, J, K, 7, B, G, 1, Z, 8, 4, F, 6, 5, 9, I2, I, 92
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · chains B, C, D
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 | 767 | 0.83 | 0.86 | 69 | DGD |
| 2 | 436 | 0.78 | 0.85 | 45 | CL0, CLA |
| 3 | 403 | 0.78 | 0.86 | 44 | CLA |
| 4 | 685 | 0.72 | 0.78 | 94 | CLA |
| 5 | 674 | 0.71 | 0.78 | 62 | CLA |
Interfaces
51 interfaces between chains.
- A–B · 3489 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1616 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1336 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 1110 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1095 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- P12154 · 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 1.00
- P09144 · 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 1.00
- Q39615 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit II… · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q00914 · AlphaFold monomer V2.0 prediction for photosystem I iron-sulfur center (Q00914) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P12352 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit IV… · a predicted model of the same protein · chain E against A, TM-score 0.96
- P12356 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit III… · a predicted model of the same protein · chain F against A, TM-score 0.95
- P59777 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit IX (P59777) · a predicted model of the same protein · chain J against A, TM-score 0.94
- P14225 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit psak… · a predicted model of the same protein · chain K against A, TM-score 0.83
- P14224 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit V… · a predicted model of the same protein · chain G against A, TM-score 0.80
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 P12154
- Every structure of UniProt P09144
- Every structure of UniProt Q00914
- Every structure of UniProt Q39615
- Every structure of UniProt P12352
- Every structure of UniProt P12356
- Every structure of UniProt P14224
- Every structure of UniProt A8IFG7
- Every structure of UniProt P59777
- Every structure of UniProt A8IL32
- Every structure of UniProt P14225
- Every structure of UniProt Q05093
- Every structure of UniProt A8JF10
- Every structure of UniProt Q84Y02
- Every structure of UniProt Q75VY7
- Every structure of UniProt Q75VZ0
- Every structure of UniProt Q75VY8
- Every structure of UniProt Q75VY6
- Every structure of UniProt A8ITV3
- Elsewhere: RCSB PDB 7ZQ9 · PDBe 7ZQ9 · UniProt P12154 · UniProt P09144 · UniProt Q00914 · UniProt Q39615 · UniProt P12352 · UniProt P12356 · UniProt P14224 · UniProt A8IFG7 · UniProt P59777 · UniProt A8IL32 · UniProt P14225 · UniProt Q05093 · UniProt A8JF10 · UniProt Q84Y02 · UniProt Q75VY7 · UniProt Q75VZ0 · UniProt Q75VY8 · UniProt Q75VY6 · UniProt A8ITV3
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