Research workbench
Photosystem I of a temperature sensitive mutant chlamydomonas reinhardtii
Analyse Photosystem I of a temperature sensitive mutant chlamydomonas reinhardtii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BLX
- Type
- protein
- Length
- 3,989 residues
- Chains
- 19
- 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
- P12154, P09144, Q00914, Q39615, P12352, P12356, P14224, A8IFG7, P59777, P14225, A8IL32, Q7DM26, Q75VY9, Q84Y02, Q75VY7, Q75VZ0, Q75VY8, Q75VY6
- Ligands
- CLA, BCR, CHL, LUT, LHG, 3PH, SF4, NKP, C7Z, SPH, PQN, LMG, CL0, OCA, DAO, DGA…
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 18 distinct chains · 53% 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 | 741 | 61% helix, 5% strand | P12154 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 59% helix, 3% strand | P09144 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 20% strand | Q00914 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 144 | 18% helix, 24% strand | Q39615 |
| E | Photosystem I reaction center subunit IV, chloroplastic | protein | 63 | 0% helix, 37% strand | P12352 |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 165 | 67% helix, 5% strand | P12356 |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 74 | 69% helix, 0% strand | P14224 |
| I | Photosystem I reaction center subunit VIII | protein | 37 | 68% helix, 3% strand | A8IFG7 |
| J | Photosystem I reaction center subunit IX | protein | 39 | 74% helix, 3% strand | P59777 |
| K | Photosystem I reaction center subunit psak, chloroplastic | protein | 84 | 50% helix, 8% strand | P14225 |
| L | Psi subunit V | protein | 126 | 75% helix, 0% strand | A8IL32 |
| 1, Z | Chlorophyll a-B binding protein, chloroplastic | protein | 194 | 51% helix, 2% strand | Q7DM26 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 51% helix, 1% strand | Q75VY9 |
| 7 | Chlorophyll a-B binding protein, chloroplastic | protein | 213 | 53% helix, 1% strand | Q84Y02 |
| 8 | Chlorophyll a-B binding protein, chloroplastic | protein | 217 | 53% helix, 0% strand | Q75VY7 |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 210 | 51% helix, 2% strand | Q75VZ0 |
| 5 | Chlorophyll a-B binding protein, chloroplastic | protein | 227 | 46% helix, 5% strand | Q75VY8 |
| 6 | Chlorophyll a-B binding protein, chloroplastic | protein | 229 | 45% helix, 5% strand | Q75VY6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 197 copies · chains A, B, J, 3, K, 7, L, F, I, G, 1, 8, Z, 4, 5, 6
- BCR · Beta-carotene · ligand · 31 copies · chains A, B, G, F, J, I, K, L, 3, 5, 7, 8, 4, 6
- CHL · Chlorophyll B · ligand · 20 copies · chains B, 1, 8, Z, 4, 3, 7, 5, 6
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 17 copies · chains 1, Z, 3, 7, 8, 4, 5, 6
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains A, B, 1, 8, Z, 3, 7, 4, 6, 5
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 4 copies · chains 3, 7, 8, 5, 6
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- NKP · (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate · ligand · 3 copies · chains A, 3, 8
- C7Z · (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E}, 9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol · ligand · 3 copies · chains A, J, G, 1, 5, 6
- SPH · Sphingosine · ligand · 3 copies · chains A, K, 3, 7, 4
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains A, J, 7, F
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- OCA · Octanoic acid (caprylic acid) · ligand
- DAO · Lauric acid · ligand · chains K
- DGA · Diacyl glycerol · ligand · chains A, 7
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C, D
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · chains A, B, F
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains 1, 8
- QTB · (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one · ligand · chains Z
- PLM · Palmitic acid · ligand · chains 7, 8
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains 8
- CA · Calcium ion · metal · chains B
- LMT · Dodecyl-beta-D-maltoside · additive · 7 copies · chains A, 3, B, 1, F, 8, G, 4
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 | 1017 | 0.83 | 0.83 | 89 | CLA, DGD |
| 2 | 543 | 0.81 | 0.86 | 63 | CL0, CLA |
| 3 | 1199 | 0.75 | 0.77 | 138 | CLA |
| 4 | 421 | 0.71 | 0.82 | 50 | empty |
| 5 | 654 | 0.70 | 0.78 | 86 | CLA, LHG |
Interfaces
39 interfaces between chains.
- A–B · 3519 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1625 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1120 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1099 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1023 Ų buried · 11 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 0.97
- 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 0.96
- 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
- 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 0.91
- 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
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 P14225
- Every structure of UniProt A8IL32
- Every structure of UniProt Q7DM26
- Every structure of UniProt Q75VY9
- 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
- Elsewhere: RCSB PDB 7BLX · PDBe 7BLX · UniProt P12154 · UniProt P09144 · UniProt Q00914 · UniProt Q39615 · UniProt P12352 · UniProt P12356 · UniProt P14224 · UniProt A8IFG7 · UniProt P59777 · UniProt P14225 · UniProt A8IL32 · UniProt Q7DM26 · UniProt Q75VY9 · UniProt Q84Y02 · UniProt Q75VY7 · UniProt Q75VZ0 · UniProt Q75VY8 · UniProt Q75VY6
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