Research workbench
Structure of plant photosystem I-light harvesting complex I supercomplex
Analyse Structure of plant photosystem I-light harvesting complex I supercomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DKZ
- Type
- protein
- Length
- 3,200 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, A0A0F6NFW5, A0A0F6NGI2, P10793, E1C9K6, A0A0M3KL12, P17227, D5MAL3, E1C9L3
- Ligands
- CLA, BCR, CHL, LHG, LMG, LUT, XAT, SF4, DGD, PQN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 16 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | LHCA1 | protein | 195 | 56% helix, 2% strand | — |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 204 | 50% helix, 1% strand | Q41038 |
| 3 | Chlorophyll a-B binding protein 3, chloroplastic | protein | 216 | 49% helix, 2% strand | Q32904 |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 195 | 51% helix, 1% strand | Q9SQL2 |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 60% helix, 5% strand | A0A0F6NFW5 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 61% helix, 3% strand | A0A0F6NGI2 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | P10793 |
| D | Psad | protein | 140 | 19% helix, 28% strand | — |
| E | Psae | protein | 63 | 5% helix, 35% strand | E1C9K6 |
| F | Psi-F | protein | 152 | 67% helix, 5% strand | A0A0M3KL12 |
| G | Psag | protein | 95 | 62% helix, 4% strand | — |
| H | Psah | protein | 88 | 49% helix, 1% strand | — |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 83% helix, 0% strand | P17227 |
| J | Photosystem I reaction center subunit IX | protein | 39 | 74% helix, 3% strand | D5MAL3 |
| L | Psal | protein | 151 | 63% helix, 4% strand | — |
| K | Psi-K | protein | 77 | 52% helix, 6% strand | E1C9L3 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 140 copies · chains 1, 4, 2, 3, F, A, B, J, K, L, H, I, G
- BCR · Beta-carotene · ligand · 26 copies · chains 1, G, 2, 3, 4, A, K, B, F, I, J, L, H
- CHL · Chlorophyll B · ligand · 12 copies · chains 1, 2, 4, 3
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 7 copies · chains 1, 4, 2, 3, A, B, F, G
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 5 copies · chains 2, 4, B, G, F, 1
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 4 copies · chains 1, 2, 3, 4
- 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 · 4 copies · chains 1, 2, 3, 4, F
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains 4, F, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 8 copies · chains 4, A, F, B, J
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains 2, J, A
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 | 668 | 0.83 | 0.86 | 73 | CLA |
| 2 | 1156 | 0.81 | 0.82 | 105 | CLA, DGD |
| 3 | 380 | 0.77 | 0.86 | 42 | CLA |
| 4 | 397 | 0.73 | 0.84 | 43 | empty |
| 5 | 825 | 0.73 | 0.78 | 73 | empty |
Interfaces
35 interfaces between chains.
- A–B · 3497 Ų buried · 43 hydrogen bonds · protein-protein
- H–L · 2002 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1629 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1495 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 962 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DKZ · Structure of plant photosystem I-light harvesting complex I supercomplex · the same entry in another collection · chain K against K, 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 A0A0F6NFW5
- Every structure of UniProt A0A0F6NGI2
- Every structure of UniProt P10793
- Every structure of UniProt E1C9K6
- Every structure of UniProt A0A0M3KL12
- Every structure of UniProt P17227
- Every structure of UniProt D5MAL3
- Every structure of UniProt E1C9L3
- Elsewhere: RCSB PDB 7DKZ · PDBe 7DKZ · UniProt Q41038 · UniProt Q32904 · UniProt Q9SQL2 · UniProt A0A0F6NFW5 · UniProt A0A0F6NGI2 · UniProt P10793 · UniProt E1C9K6 · UniProt A0A0M3KL12 · UniProt P17227 · UniProt D5MAL3 · UniProt E1C9L3
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