Research workbench
Structure of photosystem I supercomplex with light-harvesting complexes I and II
Analyse Structure of photosystem I supercomplex with light-harvesting complexes I and II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZJI
- Type
- protein
- Length
- 4,087 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein, chloroplastic; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- B6SSN3, B6T892, B6SUC4, B6SZR1, P04966, A0A059Q6U2, B4FAW3, A0A1D6HY75, B6SRI3, B6U534, O65101, P30980, P62596, B6TR16, B6STT2, B6SQZ7, B6TXS5, P12329, B6T1H1
- Ligands
- CLA, CHL, BCR, LUT, LHG, XAT, LMG, SF4, NEX, PQN, LMU, DGD, CL0
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 20 distinct chains · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 196 | 53% helix, 1% strand | B6SSN3 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 207 | 53% helix, 1% strand | B6T892 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 221 | 48% helix, 1% strand | B6SUC4 |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 199 | 47% helix, 1% strand | B6SZR1 |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 742 | 59% helix, 4% strand | P04966 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 58% helix, 2% strand | A0A059Q6U2 |
| C | Photosystem I subunit VII | protein | 81 | 10% helix, 21% strand | — |
| D | Photosystem I reaction center subunit II | protein | 142 | 15% helix, 24% strand | B4FAW3 |
| E | Photosystem I reaction center subunit IV a | protein | 68 | 4% helix, 32% strand | A0A1D6HY75 |
| F | Photosystem I reaction center subunit III | protein | 158 | 63% helix, 5% strand | B6SRI3 |
| G | Photosystem I reaction center subunit V | protein | 97 | 60% helix, 2% strand | B6U534 |
| H | Photosystem I reaction center subunit VI, chloroplastic | protein | 95 | 37% helix, 0% strand | O65101 |
| I | Photosystem I reaction center subunit VIII | protein | 33 | 73% helix, 0% strand | P30980 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 71% helix, 2% strand | P62596 |
| K | Photosystem I reaction center subunit psak | protein | 84 | 44% helix, 0% strand | B6TR16 |
| L | Photosystem I reaction center subunit XI | protein | 166 | 52% helix, 3% strand | B6STT2 |
| O | 16KDA membrane protein | protein | 76 | 46% helix, 0% strand | B6SQZ7 |
| N | Photosystem I reaction center subunit N | protein | 84 | 45% helix, 0% strand | B6TXS5 |
| X, Z | Chlorophyll a-B binding protein 1, chloroplastic | protein | 218 | 52% helix, 3% strand | P12329 |
| Y | Chlorophyll a-B binding protein, chloroplastic | protein | 228 | 47% helix, 2% strand | B6T1H1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 171 copies · chains 1, 4, 2, 3, F, A, B, J, N, K, O, L, H, I, G, X, Z, Y
- CHL · Chlorophyll B · ligand · 30 copies · chains 1, 4, G, 2, 3, N, X, Y, Z, O
- BCR · Beta-carotene · ligand · 26 copies · chains 1, G, 2, 3, 4, A, O, B, J, N, F, I, K, L, H
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 11 copies · chains 1, 4, F, 2, 3, X, Y, Z
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 8 copies · chains 1, 4, 2, 3, A, B, X, O, Y, Z
- 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 · 7 copies · chains 1, 2, 3, 4, F, X, Z, Y, O
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 5 copies · chains 1, 4, 2, N, F, G
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 3 copies · chains X, Y, K, Z
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- LMU · Dodecyl-alpha-D-maltoside · ligand · 2 copies · chains A, N, B, G
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains B, C, F, J
- CL0 · Chlorophyll A isomer · ligand · chains 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 | 629 | 0.82 | 0.86 | 70 | CL0, CLA |
| 2 | 807 | 0.78 | 0.82 | 60 | DGD |
| 3 | 390 | 0.78 | 0.86 | 43 | CLA |
| 4 | 1102 | 0.76 | 0.78 | 143 | CLA |
| 5 | 399 | 0.75 | 0.85 | 55 | empty |
Interfaces
52 interfaces between chains.
- A–B · 3519 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 1981 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1638 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1624 Ų buried · 33 hydrogen bonds · protein-protein
- A–N · 1486 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 1 modified (covalent ligand, disulfide, phosphorylation).
Compared structures
- 5ZJI · Structure of photosystem I supercomplex with light-harvesting complexes I and II · the same entry in another collection · chain G against G, 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 B6SSN3
- Every structure of UniProt B6T892
- Every structure of UniProt B6SUC4
- Every structure of UniProt B6SZR1
- Every structure of UniProt P04966
- Every structure of UniProt A0A059Q6U2
- Every structure of UniProt B4FAW3
- Every structure of UniProt A0A1D6HY75
- Every structure of UniProt B6SRI3
- Every structure of UniProt B6U534
- Every structure of UniProt O65101
- Every structure of UniProt P30980
- Every structure of UniProt P62596
- Every structure of UniProt B6TR16
- Every structure of UniProt B6STT2
- Every structure of UniProt B6SQZ7
- Every structure of UniProt B6TXS5
- Every structure of UniProt P12329
- Every structure of UniProt B6T1H1
- Elsewhere: RCSB PDB 5ZJI · PDBe 5ZJI · UniProt B6SSN3 · UniProt B6T892 · UniProt B6SUC4 · UniProt B6SZR1 · UniProt P04966 · UniProt A0A059Q6U2 · UniProt B4FAW3 · UniProt A0A1D6HY75 · UniProt B6SRI3 · UniProt B6U534 · UniProt O65101 · UniProt P30980 · UniProt P62596 · UniProt B6TR16 · UniProt B6STT2 · UniProt B6SQZ7 · UniProt B6TXS5 · UniProt P12329 · UniProt B6T1H1
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