Research workbench
The structure of a plant photosystem I supercomplex at 3.4 ångström resolution
Analyse The structure of a plant photosystem I supercomplex at 3.4 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O01
- Type
- protein
- Length
- 3,043 residues
- Chains
- 17
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- UniProt
- P05310, P05311, P10793, P12353, Q9S831, P12355, P12357, P22179, P17227, P17230, Q41385, Q84U30, Q01667, Q41038, Q9SY97, Q9SQL2
- Ligands
- CLA, BCR, SF4, PQN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 17 distinct chains · 26% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 | protein | 728 | 28% helix, 1% strand | P05310 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 732 | 33% helix, 1% strand | P05311 |
| C | Photosystem I iron-sulfur center | protein | 80 | 0% helix, 3% strand | P10793 |
| D | Photosystem I reaction center subunit II, chloroplast | protein | 138 | 6% helix, 11% strand | P12353 |
| E | Photosystem I reaction center subunit IV a, chloroplast | protein | 62 | 0% helix, 6% strand | Q9S831 |
| F | Photosystem I reaction center subunit III, chloroplast | protein | 154 | 24% helix, 1% strand | P12355 |
| G | Photosystem I reaction center subunit V, chloroplast | protein | 95 | 23% helix, 0% strand | P12357 |
| H | Photosystem I reaction center subunit VI, chloroplast | protein | 75 | 15% helix, 0% strand | P22179 |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 47% helix, 0% strand | P17227 |
| J | Photosystem I reaction center subunit IX | protein | 42 | 45% helix, 0% strand | P17230 |
| K | Photosystem I reaction center subunit psak, chloroplast | protein | 37 | 59% helix, 0% strand | — |
| L | Photosystem I reaction center subunit XI, chloroplast | protein | 164 | 21% helix, 0% strand | Q41385 |
| N | Photosystem I-N subunit | protein | 85 | 8% helix, 0% strand | Q84U30 |
| 1 | AT3G54890 | protein | 175 | 22% helix, 0% strand | Q01667 |
| 2 | Type II chlorophyll A/B binding protein from photosystem I | protein | 166 | 31% helix, 0% strand | Q41038 |
| 3 | Psi type III chlorophyll A/B-binding protein | protein | 115 | 36% helix, 0% strand | Q9SY97 |
| 4 | Psi light-harvesting antenna chlorophyll A/B-binding protein | protein | 165 | 30% helix, 0% strand | Q9SQL2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 168 copies · chains A, J, B, L, F, K, I, H, G, 1, 4, 2, 3
- BCR · Beta-carotene · ligand · 5 copies · chains A, B, F, I, L
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · 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 | 1101 | 0.83 | 0.83 | 113 | CLA |
| 2 | 1053 | 0.81 | 0.82 | 92 | CLA |
| 3 | 1032 | 0.80 | 0.81 | 113 | empty |
| 4 | 1081 | 0.79 | 0.80 | 117 | CLA |
| 5 | 969 | 0.79 | 0.80 | 70 | empty |
Interfaces
37 interfaces between chains.
- A–B · 3283 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1297 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 1136 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1090 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1022 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 2O01 · The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution · 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 P05310
- Every structure of UniProt P05311
- Every structure of UniProt P10793
- Every structure of UniProt P12353
- Every structure of UniProt Q9S831
- Every structure of UniProt P12355
- Every structure of UniProt P12357
- Every structure of UniProt P22179
- Every structure of UniProt P17227
- Every structure of UniProt P17230
- Every structure of UniProt Q41385
- Every structure of UniProt Q84U30
- Every structure of UniProt Q01667
- Every structure of UniProt Q41038
- Every structure of UniProt Q9SY97
- Every structure of UniProt Q9SQL2
- Elsewhere: RCSB PDB 2O01 · PDBe 2O01 · UniProt P05310 · UniProt P05311 · UniProt P10793 · UniProt P12353 · UniProt Q9S831 · UniProt P12355 · UniProt P12357 · UniProt P22179 · UniProt P17227 · UniProt P17230 · UniProt Q41385 · UniProt Q84U30 · UniProt Q01667 · UniProt Q41038 · UniProt Q9SY97 · UniProt Q9SQL2
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