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The structure of plant photosystem I super-complex at 2.6 ångström resolution.
Analyse The structure of plant photosystem I super-complex at 2.6 ångström resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L8R
- Type
- protein
- Length
- 3,230 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LHCA1; Chlorophyll a-B binding protein, chloroplastic; Chlorophyll a-B binding protein 3…
- EC
- 1.97.1.12
- UniProt
- Q41038, Q32904, Q9SQL2, P05310, A0A0F6NGI2, P10793, E1C9K6, A0A0M3KL12, A0A0M3KL10, P17227, D5MAL3, E1C9L3, E1C9L1
- Ligands
- CLA, BCR, LMG, CHL, LUT, LHG, DGD, SF4, XAT, PQN, CL0, ZEX, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 16 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | LHCA1 | protein | 193 | 56% helix, 2% strand | — |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 208 | 51% helix, 1% strand | Q41038 |
| 3 | Chlorophyll a-B binding protein 3, chloroplastic | protein | 221 | 49% helix, 0% strand | Q32904 |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 198 | 51% helix, 2% strand | Q9SQL2 |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 743 | 60% helix, 5% strand | P05310 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 62% helix, 2% strand | A0A0F6NGI2 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | P10793 |
| D | Psad | protein | 143 | 17% helix, 27% strand | — |
| E | Putative uncharacterized protein | protein | 66 | 5% helix, 35% strand | E1C9K6 |
| F | Photosystem I reaction center subunit III | protein | 154 | 69% helix, 5% strand | A0A0M3KL12 |
| G | Psag | protein | 97 | 58% helix, 4% strand | — |
| H | Photosystem I reaction center subunit VI | protein | 88 | 45% helix, 1% strand | A0A0M3KL10 |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 87% helix, 0% strand | P17227 |
| J | Photosystem I reaction center subunit IX | protein | 42 | 69% helix, 2% strand | D5MAL3 |
| K | Photosystem I reaction center subunit X psak | protein | 77 | 53% helix, 6% strand | E1C9L3 |
| L | Putative uncharacterized protein | protein | 157 | 59% helix, 5% strand | E1C9L1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 142 copies · chains 1, 4, 2, 3, F, A, B, J, K, L, I, H, G
- BCR · Beta-carotene · ligand · 27 copies · chains 1, 2, 3, 4, A, B, K, G, F, I, L, J, H
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 20 copies · chains 1, 4, B, 2, J, F, A, G
- CHL · Chlorophyll B · ligand · 13 copies · chains 1, G, 4, 2, 3
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 7 copies · chains 1, 2, 3, 4, A, J
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 7 copies · chains 1, 4, B, G, 2, 3, A, I
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 5 copies · chains 2, 4, 1, B, C, G, F, J
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 2 copies · chains 2, 4, F
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- ZEX · (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol · ligand · chains 1, 4, F
- CA · Calcium ion · metal · 2 copies · chains 3, A, B
- LMT · Dodecyl-beta-D-maltoside · additive · 10 copies · chains 2, 3, 1, 4, A, B, F, G, J
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 | 811 | 0.84 | 0.86 | 78 | CL0, CLA |
| 2 | 892 | 0.82 | 0.84 | 74 | DGD |
| 3 | 680 | 0.78 | 0.83 | 73 | CLA |
| 4 | 972 | 0.77 | 0.79 | 84 | empty |
| 5 | 941 | 0.75 | 0.78 | 132 | CLA, LHG |
Interfaces
36 interfaces between chains.
- A–B · 3491 Ų buried · 46 hydrogen bonds · protein-protein
- H–L · 1961 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1630 Ų buried · 26 hydrogen bonds · protein-protein
- B–G · 1596 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 995 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5L8R · The structure of plant photosystem I super-complex at 2.6 angstrom resolution. · 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 Q41038
- Every structure of UniProt Q32904
- Every structure of UniProt Q9SQL2
- Every structure of UniProt P05310
- Every structure of UniProt A0A0F6NGI2
- Every structure of UniProt P10793
- Every structure of UniProt E1C9K6
- Every structure of UniProt A0A0M3KL12
- Every structure of UniProt A0A0M3KL10
- Every structure of UniProt P17227
- Every structure of UniProt D5MAL3
- Every structure of UniProt E1C9L3
- Every structure of UniProt E1C9L1
- Elsewhere: RCSB PDB 5L8R · PDBe 5L8R · UniProt Q41038 · UniProt Q32904 · UniProt Q9SQL2 · UniProt P05310 · UniProt A0A0F6NGI2 · UniProt P10793 · UniProt E1C9K6 · UniProt A0A0M3KL12 · UniProt A0A0M3KL10 · UniProt P17227 · UniProt D5MAL3 · UniProt E1C9L3 · UniProt E1C9L1
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