Research workbench
Cyanobacterial psi monomer from T. elongatus by single particle cryo- EM at 3.2 a resolution
Analyse Cyanobacterial psi monomer from T. elongatus by single particle cryo- EM at 3.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LU1
- Type
- protein
- Length
- 1,986 residues
- Chains
- 10
- 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, Q8DGB4, P0A403
- Ligands
- CLA, BCR, SF4, PQN, LHG, LMG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 46% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 745 | 53% helix, 5% strand | P0A405 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 713 | 50% helix, 1% strand | P0A407 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 14% helix, 21% strand | P0A415 |
| D | Photosystem I reaction center subunit II | protein | 138 | 11% helix, 26% strand | P0A420 |
| E | Photosystem I reaction center subunit IV | protein | 69 | 0% helix, 29% strand | P0A423 |
| F | Photosystem I reaction center subunit III | protein | 29 | 66% helix, 0% strand | P0A401 |
| I | Photosystem I reaction center subunit VIII | protein | 38 | 55% helix, 0% strand | P0A427 |
| J | Photosystem I reaction center subunit IX | protein | 8 | 38% helix, 0% strand | P0A429 |
| L | Photosystem I reaction center subunit XI | protein | 135 | 52% helix, 4% strand | Q8DGB4 |
| M | Photosystem I reaction center subunit XII | protein | 31 | 68% helix, 0% strand | P0A403 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 82 copies · chains A, B, J, L, I, F, M
- BCR · Beta-carotene · ligand · 26 copies · chains A, J, B, F, I, L, M
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, E
- 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 | 1056 | 0.83 | 0.83 | 96 | CLA |
| 2 | 725 | 0.77 | 0.82 | 72 | LMG |
| 3 | 66 | 0.73 | 0.98 | 18 | SF4 |
| 4 | 70 | 0.73 | 0.97 | 20 | SF4 |
| 5 | 73 | 0.72 | 0.96 | 19 | SF4 |
Interfaces
20 interfaces between chains.
- A–B · 3556 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1531 Ų buried · 15 hydrogen bonds · protein-protein
- B–M · 999 Ų buried · 3 hydrogen bonds · protein-protein
- B–I · 859 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 837 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LU1 · Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A… · the same entry in another collection · chain M against M, TM-score 1.00
- P0A405 · 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
- P0A407 · 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 0.99
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 Q8DGB4
- Every structure of UniProt P0A403
- Elsewhere: RCSB PDB 6LU1 · PDBe 6LU1 · UniProt P0A405 · UniProt P0A407 · UniProt P0A415 · UniProt P0A420 · UniProt P0A423 · UniProt P0A401 · UniProt P0A427 · UniProt P0A429 · UniProt Q8DGB4 · UniProt P0A403
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