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Cryo-EM structure of the tetrameric photosystem I from a heterocyst- forming cyanobacterium anabaena sp. PCC7120
Analyse Cryo-EM structure of the tetrameric photosystem I from a heterocyst- forming… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K61
- Type
- protein
- Length
- 4,542 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I 4.8 kda protein…
- EC
- 1.97.1.12
- UniProt
- P58576, P58566, P58565, P0A410, P58573, P58575, P58564, P58568, P58583, P58560, P58577, Q8YNB0
- Ligands
- CLA, BCR, SF4, LHG, PQN, SQD, LMG, CL0
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 14 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 60% helix, 5% strand | P58576 |
| X, x | Photosystem I 4.8 kda protein | protein | 31 | 68% helix, 0% strand | P58566 |
| B, b | Photosystem I P700 chlorophyll a apoprotein A2 1 (EC 1.97.1.12) | protein | 740 | 60% helix, 3% strand | P58565 |
| C, c | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | P0A410 |
| D | Photosystem I reaction center subunit II | protein | 135 | 13% helix, 29% strand | P58573 |
| E, e | Photosystem I reaction center subunit IV | protein | 61 | 0% helix, 38% strand | P58575 |
| F, f | Photosystem I reaction center subunit III | protein | 141 | 56% helix, 6% strand | P58564 |
| J, j | Photosystem I reaction center subunit IX | protein | 45 | 71% helix, 2% strand | P58568 |
| K | Photosystem I reaction center subunit psak 1 | protein | 73 | 63% helix, 3% strand | P58583 |
| I, i | Photosystem I reaction center subunit VIII | protein | 34 | 79% helix, 0% strand | P58560 |
| L, l | Photosystem I reaction center subunit XI | protein | 155 | 65% helix, 3% strand | P58577 |
| M, m | Photosystem I reaction center subunit XII | protein | 31 | 84% helix, 0% strand | Q8YNB0 |
| d | Photosystem I reaction center subunit II | protein | 136 | 13% helix, 26% strand | P58573 |
| k | Photosystem I reaction center subunit psak 1 | protein | 78 | 59% helix, 3% strand | P58583 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 188 copies · chains A, B, F, J, K, L, I, m, X, M, l, a, f, j, b, k, i, x
- BCR · Beta-carotene · ligand · 46 copies · chains A, K, B, F, J, I, L, M, a, k, b, f, j, i, l, m
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, a, b, c
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains A, X, F, a, b, i, m
- PQN · Phylloquinone · ligand · 4 copies · chains A, J, B, a, j, b
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 4 copies · chains X, B, x, b, L, m, i, l
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains X, B, b
- CL0 · Chlorophyll A isomer · ligand · 2 copies · chains A, B, a, 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 | 1103 | 0.86 | 0.86 | 103 | CL0, CLA |
| 2 | 610 | 0.82 | 0.86 | 61 | CLA |
| 3 | 982 | 0.80 | 0.81 | 79 | LMG |
| 4 | 953 | 0.80 | 0.81 | 82 | CLA, LMG |
| 5 | 82 | 0.73 | 0.96 | 25 | empty |
Interfaces
56 interfaces between chains.
- A–B · 3526 Ų buried · 42 hydrogen bonds · protein-protein
- a–b · 3523 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1653 Ų buried · 22 hydrogen bonds · protein-protein
- c–d · 1602 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1226 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 covalent (covalent ligand).
Compared structures
- 6K61 · Cryo-EM structure of the tetrameric photosystem I from a heterocyst-forming… · the same entry in another collection · chain L against L, 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 P58576
- Every structure of UniProt P58566
- 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 P58568
- Every structure of UniProt P58583
- Every structure of UniProt P58560
- Every structure of UniProt P58577
- Every structure of UniProt Q8YNB0
- Elsewhere: RCSB PDB 6K61 · PDBe 6K61 · UniProt P58576 · UniProt P58566 · UniProt P58565 · UniProt P0A410 · UniProt P58573 · UniProt P58575 · UniProt P58564 · UniProt P58568 · UniProt P58583 · UniProt P58560 · UniProt P58577 · UniProt Q8YNB0
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