MolNFT v1 · #105958 · protein
Crystal structure of plant photosystem I at 3 ångström resolution
4RKU · Photosystem I P700 chlorophyll a apoprotein A1: “Crystal structure of plant photosystem I at 3 ångström resolution”. X-ray diffraction, 11 ligands (CLA, BCR, LUT), 20 pockets (best druggability 0.80). MolNFT v1 #105958 on GenesisL1…
- PDB
- 4RKU
- Type
- protein
- Length
- 3,093 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…
- EC
- 1.97.1.12
- UniProt
- P05310, P05311, P10793, P17227, D5MAL3, E1C9L3, E1C9K7, Q41038, Q32904, Q9SQL2
- Ligands
- CLA, BCR, LUT, LHG, SF4, PQN, LMG, CL0, DGD, NEX, G3P
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 17 distinct chains · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 721 | 59% helix, 4% strand | P05310 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 731 | 59% helix, 2% strand | P05311 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 19% helix, 21% strand | P10793 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 137 | 11% helix, 20% strand | — |
| E | Photosystem I reaction center subunit IV B, chloroplastic | protein | 63 | 0% helix, 21% strand | — |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 152 | 62% helix, 1% strand | — |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 84 | 63% helix, 0% strand | — |
| H | Photosystem I reaction center subunit VI, chloroplastic | protein | 82 | 39% helix, 1% strand | — |
| I | Photosystem I reaction center subunit VIII | protein | 26 | 81% helix, 0% strand | P17227 |
| J | Photosystem I reaction center subunit IX | protein | 40 | 65% helix, 0% strand | D5MAL3 |
| K | Photosystem I reaction center subunit X psak | protein | 66 | 53% helix, 0% strand | E1C9L3 |
| L | Photosystem I reaction center subunit XI, chloroplastic | protein | 163 | 52% helix, 3% strand | — |
| N | Photosystem I-N subunit | protein | 85 | 8% helix, 0% strand | E1C9K7 |
| 1 | Chlorophyll a-B binding protein 6A, chloroplastic | protein | 171 | 57% helix, 0% strand | — |
| 2 | Type II chlorophyll A/B binding protein from photosystem I | protein | 146 | 47% helix, 0% strand | Q41038 |
| 3 | Chlorophyll a-B binding protein 3, chloroplastic | protein | 151 | 50% helix, 0% strand | Q32904 |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 195 | 45% helix, 0% strand | Q9SQL2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 157 copies · chains A, F, J, B, 3, K, L, I, H, G, 1, 4, 2
- BCR · Beta-carotene · ligand · 21 copies · chains A, B, G, F, J, I, L
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains 1, 2, 4, F
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains A, B, 1, 4, 2
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains G, 1, F, J
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains 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 · chains 4
- G3P · Sn-glycerol-3-phosphate · ligand · chains 4
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 | 788 | 0.80 | 0.83 | 78 | DGD |
| 2 | 485 | 0.79 | 0.86 | 54 | CL0, CLA |
| 3 | 866 | 0.77 | 0.80 | 68 | empty |
| 4 | 690 | 0.75 | 0.81 | 78 | CLA |
| 5 | 1167 | 0.73 | 0.76 | 138 | CLA, LMG |
Interfaces
37 interfaces between chains.
- A–B · 3511 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 1845 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1564 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 1159 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 972 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4RKU · Crystal structure of plant Photosystem I at 3 Angstrom resolution · the same entry in another collection · chain 4 against 4, 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 P17227
- Every structure of UniProt D5MAL3
- Every structure of UniProt E1C9L3
- Every structure of UniProt E1C9K7
- Every structure of UniProt Q41038
- Every structure of UniProt Q32904
- Every structure of UniProt Q9SQL2
- Elsewhere: RCSB PDB 4RKU · PDBe 4RKU · UniProt P05310 · UniProt P05311 · UniProt P10793 · UniProt P17227 · UniProt D5MAL3 · UniProt E1C9L3 · UniProt E1C9K7 · UniProt Q41038 · UniProt Q32904 · UniProt Q9SQL2
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