MolNFT v1 · #165327 · protein
Cryo- EM structure of the thermosynechococcus elongatus photosystem I in the presence of cytochrome C6
6TRD · Photosystem I P700 chlorophyll a apoprotein A1: “Cryo- EM structure of the thermosynechococcus elongatus photosystem I in the presence of cytochrome C6”. Electron microscopy, 8 ligands (CLA, BCR, LHG), 20 pockets (best druggability…
- PDB
- 6TRD
- Type
- protein
- Length
- 6,849 residues
- Chains
- 36
- 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
- P0A405, P0A407, P0A415, P0A420, P0A423, P0A401, P0A427, P0A429, P0A425, Q8DGB4, P0A403, Q8DKP6
- Ligands
- CLA, BCR, LHG, SF4, PQN, CL0, LMG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a, 1 | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 746 | 58% helix, 4% strand | P0A405 |
| B, b, 2 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 740 | 59% helix, 3% strand | P0A407 |
| C, c, 3 | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 13% helix, 21% strand | P0A415 |
| D, d, 4 | Photosystem I reaction center subunit II | protein | 138 | 13% helix, 27% strand | P0A420 |
| E, e, 5 | Photosystem I reaction center subunit IV | protein | 70 | 4% helix, 33% strand | P0A423 |
| F, f, 6 | Photosystem I reaction center subunit III | protein | 141 | 52% helix, 4% strand | P0A401 |
| I, i, 7 | Photosystem I reaction center subunit VIII | protein | 38 | 68% helix, 3% strand | P0A427 |
| J, j, 8 | Photosystem I reaction center subunit IX | protein | 41 | 71% helix, 2% strand | P0A429 |
| K, k, 9 | Photosystem I reaction center subunit psak | protein | 79 | 58% helix, 0% strand | P0A425 |
| L, l, 0 | Photosystem I reaction center subunit XI | protein | 152 | 61% helix, 5% strand | Q8DGB4 |
| M, m, y | Photosystem I reaction center subunit XII | protein | 31 | 84% helix, 0% strand | P0A403 |
| X, x, z | Photosystem I 4.8K protein | protein | 27 | 81% helix, 0% strand | Q8DKP6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 288 copies · chains A, B, F, J, K, L, I, 2, y, M, l, k, X, 7, 0, a, b, f, j, i, m, 9, x, 1, 6, 8, z
- BCR · Beta-carotene · ligand · 72 copies · chains A, B, J, F, I, K, L, l, M, a, b, f, j, i, k, m, 1, 2, 6, 8, 7, 9, 0, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 15 copies · chains A, E, B, X, L, 7, 0, I, M, l, a, e, b, x, i, m, 1, 5, y, 2, z
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, a, b, c, 1, 2, 3
- PQN · Phylloquinone · ligand · 6 copies · chains A, J, B, a, j, b, 1, 8, 2
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains A, B, a, b, 1, 2
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains B, b, 2
- CA · Calcium ion · metal · 6 copies · chains B, L, l, b, 0, 2
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 | 922 | 0.84 | 0.85 | 93 | BCR, CLA |
| 2 | 784 | 0.84 | 0.86 | 79 | CL0, CLA |
| 3 | 741 | 0.83 | 0.86 | 77 | CL0, CLA |
| 4 | 689 | 0.82 | 0.86 | 68 | CL0, CLA |
| 5 | 771 | 0.79 | 0.82 | 73 | LMG |
Interfaces
96 interfaces between chains.
- A–B · 3558 Ų buried · 41 hydrogen bonds · protein-protein
- 1–2 · 3534 Ų buried · 40 hydrogen bonds · protein-protein
- a–b · 3497 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 23 hydrogen bonds · protein-protein
- 3–4 · 1503 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 covalent, 6 modified, 3 disulfide (covalent ligand, formylation, disulfide).
Compared structures
- 6TRD · Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of… · the same entry in another collection · chain M against M, 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 P0A405
- Every structure of UniProt P0A407
- Every structure of UniProt P0A415
- Every structure of UniProt P0A420
- Every structure of UniProt P0A423
- Every structure of UniProt P0A401
- Every structure of UniProt P0A427
- Every structure of UniProt P0A429
- Every structure of UniProt P0A425
- Every structure of UniProt Q8DGB4
- Every structure of UniProt P0A403
- Every structure of UniProt Q8DKP6
- Elsewhere: RCSB PDB 6TRD · PDBe 6TRD · UniProt P0A405 · UniProt P0A407 · UniProt P0A415 · UniProt P0A420 · UniProt P0A423 · UniProt P0A401 · UniProt P0A427 · UniProt P0A429 · UniProt P0A425 · UniProt Q8DGB4 · UniProt P0A403 · UniProt Q8DKP6
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