MolNFT v1 · #53365 · protein
Improved model of plant photosystem I
2WSF · AT3G54890: “Improved model of plant photosystem I”. X-ray diffraction, 9 ligands (CLA, LMU, BCR), 20 pockets (best druggability 0.86). MolNFT v1 #53365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WSF
- Type
- protein
- Length
- 3,181 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT3G54890; Type II chlorophyll A/B binding protein from photosystem I; LHCA3; Chlorophyll…
- UniProt
- Q9C5R7, Q41038, Q9SQL2, P05310, P05311, P10793, P12353, Q9S831, P12355, P12357, P22179, P17227, P17230, P36886, Q41385, Q84U30
- Ligands
- CLA, LMU, BCR, SF4, PQN, LMG, UNL, GLC, FRU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 18 distinct chains · 28% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | AT3G54890 | protein | 165 | 35% helix, 0% strand | Q9C5R7 |
| 2 | Type II chlorophyll A/B binding protein from photosystem I | protein | 176 | 39% helix, 0% strand | Q41038 |
| 3 | LHCA3 | protein | 153 | 25% helix, 0% strand | — |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 166 | 35% helix, 0% strand | Q9SQL2 |
| A | Photosystem I P700 chlorophyll a apoprotein A1 | protein | 730 | 37% helix, 1% strand | P05310 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 733 | 33% helix, 2% strand | P05311 |
| C | Photosystem I iron-sulfur center | protein | 81 | 0% helix, 0% strand | P10793 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 138 | 3% helix, 8% strand | P12353 |
| E | Photosystem I reaction center subunit IV a, chloroplastic | protein | 65 | 0% helix, 14% strand | Q9S831 |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 154 | 25% helix, 1% strand | P12355 |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 95 | 20% helix, 0% strand | P12357 |
| H | Photosystem I reaction center subunit VI, chloroplastic | protein | 69 | 4% 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 | 14% helix, 0% strand | P17230 |
| K | Photosystem I reaction center subunit psak, chloroplastic | protein | 84 | 24% helix, 0% strand | P36886 |
| L | Photosystem I reaction center subunit XI, chloroplastic | protein | 162 | 25% helix, 1% strand | Q41385 |
| N | Photosystem I-N subunit | protein | 85 | 0% helix, 0% strand | Q84U30 |
| R | Photosystem I-N subunit | protein | 53 | 36% helix, 4% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 173 copies · chains 1, 2, 3, 4, F, J, A, B, K, L, G, I, H, R
- LMU · Dodecyl-alpha-D-maltoside · ligand · 48 copies · chains 2, 4, A, K, R, B, D, G, H, L
- BCR · Beta-carotene · ligand · 16 copies · chains A, B, H, I, L, F, G, J
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains B, C
- UNL · Unknown ligand · ligand
- GLC · alpha-D-glucopyranose · sugar · 13 copies · chains 2, 3
- FRU · beta-D-fructofuranose · sugar · 13 copies · chains H
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 | 1016 | 0.86 | 0.87 | 109 | LMG, SF4 |
| 2 | 900 | 0.85 | 0.86 | 93 | CLA |
| 3 | 447 | 0.79 | 0.87 | 69 | SF4 |
| 4 | 561 | 0.78 | 0.84 | 78 | empty |
| 5 | 880 | 0.77 | 0.80 | 69 | empty |
Interfaces
40 interfaces between chains.
- A–B · 3605 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 1106 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1028 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 879 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 2WSF · Improved Model of Plant Photosystem I · the same entry in another collection · chain F against F, 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 Q9C5R7
- Every structure of UniProt Q41038
- Every structure of UniProt Q9SQL2
- 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 P36886
- Every structure of UniProt Q41385
- Every structure of UniProt Q84U30
- Elsewhere: RCSB PDB 2WSF · PDBe 2WSF · UniProt Q9C5R7 · UniProt Q41038 · UniProt Q9SQL2 · UniProt P05310 · UniProt P05311 · UniProt P10793 · UniProt P12353 · UniProt Q9S831 · UniProt P12355 · UniProt P12357 · UniProt P22179 · UniProt P17227 · UniProt P17230 · UniProt P36886 · UniProt Q41385 · UniProt Q84U30
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