Research workbench
Photosystem I from a chlorophyll D-containing cyanobacterium acaryochloris marina
Analyse Photosystem I from a chlorophyll D-containing cyanobacterium acaryochloris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DWQ
- Type
- protein
- Length
- 1,943 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I protein psad; Photosystem I P740 chlorophyll a apoprotein A1; Photosystem I…
- EC
- 1.97.1.12
- UniProt
- B0C8F1, B0C474, B0C475, B0CB42, B0C5D5, B0C7S7, B0C7S6, B0C7S4
- Ligands
- CL7, 8CT, SF4, PQN, LHG, PHO, G9R, LMG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 10 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Photosystem I protein psad | protein | 94 | 20% helix, 35% strand | B0C8F1 |
| A | Photosystem I P740 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 726 | 60% helix, 4% strand | B0C474 |
| B | Photosystem I P740 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 659 | 61% helix, 2% strand | B0C475 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 20% strand | B0CB42 |
| E | Photosystem I reaction center subunit IV | protein | 58 | 0% helix, 28% strand | B0C5D5 |
| F | Photosystem I protein psaf | protein | 103 | 43% helix, 6% strand | B0C7S7 |
| J | Photosystem I reaction center subunit IX | protein | 21 | 90% helix, 0% strand | B0C7S6 |
| L | Photosystem I protein psal | protein | 144 | 62% helix, 1% strand | B0C7S4 |
| M | Photosystem I reaction center subunit XII | protein | 30 | 83% helix, 0% strand | — |
| W | Photosystem I protein PSA27 | protein | 28 | 86% helix, 0% strand | — |
Ligands and binding sites
- CL7 · Chlorophyll D · ligand · 76 copies · chains A, B, F, J, L, W, M
- 8CT · (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene · ligand · 13 copies · chains A, B, F, J, L, W, M
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B, W
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, E
- PHO · Pheophytin A · ligand · 2 copies · chains A, B
- G9R · Chlorophyll D isomer · ligand · chains A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains B
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 | 444 | 0.79 | 0.86 | 52 | G9R, CL7 |
| 2 | 982 | 0.73 | 0.77 | 74 | empty |
| 3 | 730 | 0.73 | 0.78 | 63 | CL7 |
| 4 | 219 | 0.72 | 0.87 | 28 | PHO |
| 5 | 1149 | 0.71 | 0.75 | 96 | CL7, LHG |
Interfaces
21 interfaces between chains.
- A–B · 3473 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 868 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 844 Ų buried · 13 hydrogen bonds · protein-protein
- B–M · 827 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 771 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7DWQ · Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina · the same entry in another collection · chain W against W, TM-score 1.00
- B0C474 · 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 0.99
- B0CB42 · AlphaFold monomer V2.0 prediction for photosystem I iron-sulfur center (B0CB42) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 B0C8F1
- Every structure of UniProt B0C474
- Every structure of UniProt B0C475
- Every structure of UniProt B0CB42
- Every structure of UniProt B0C5D5
- Every structure of UniProt B0C7S7
- Every structure of UniProt B0C7S6
- Every structure of UniProt B0C7S4
- Elsewhere: RCSB PDB 7DWQ · PDBe 7DWQ · UniProt B0C8F1 · UniProt B0C474 · UniProt B0C475 · UniProt B0CB42 · UniProt B0C5D5 · UniProt B0C7S7 · UniProt B0C7S6 · UniProt B0C7S4
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