MolNFT v2 · #192960 · protein
RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution
7RF5: “RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution”. X-ray diffraction at 2.23, 16 ligands (CLA, STE, BCR). MolNFT v2 #192960 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RF5
- Type
- protein
- Length
- 5,299 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.23
- Source
- Thermosynechococcus elongatus (strain BP-1)
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DKM3, Q8DIQ0, Q9F1L5, P0A386, Q9F1R6, Q8DJI1, Q8DHJ2
- Ligands
- CLA, STE, BCR, LMG, LHG, SQD, PHO, PL9, OEY, OEX, BCT, HEM, HEC, DGD, FE2, CL
Structure
x-ray diffraction · resolution 2.23 · 26 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | — | protein | 334 | — | P0A444 |
| B, b | — | protein | 505 | — | Q8DIQ1 |
| C | — | protein | 442 | — | Q8DIF8 |
| D, d | — | protein | 341 | — | Q8CM25 |
| E, e | — | protein | 82 | — | Q8DIP0 |
| F, f | — | protein | 34 | — | Q8DIN9 |
| H | — | protein | 65 | — | Q8DJ43 |
| I, i | — | protein | 36 | — | Q8DJZ6 |
| J, j | — | protein | 36 | — | P59087 |
| K, k | — | protein | 37 | — | Q9F1K9 |
| L | — | protein | 37 | — | Q8DIN8 |
| M | — | protein | 33 | — | Q8DHA7 |
| O, o | — | protein | 244 | — | P0A431 |
| R, r | — | protein | 28 | — | Q8DKM3 |
| T, t | — | protein | 30 | — | Q8DIQ0 |
| U, u | — | protein | 97 | — | Q9F1L5 |
| V, v | — | protein | 137 | — | P0A386 |
| X | — | protein | 38 | — | Q9F1R6 |
| Y | — | protein | 27 | — | Q8DJI1 |
| Z, z | — | protein | 62 | — | Q8DHJ2 |
| c | — | protein | 451 | — | Q8DIF8 |
| h | — | protein | 63 | — | Q8DJ43 |
| l | — | protein | 36 | — | Q8DIN8 |
| m | — | protein | 32 | — | Q8DHA7 |
| x | — | protein | 39 | — | Q9F1R6 |
| y | — | protein | 30 | — | Q8DJI1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, L, B, H, M, t, C, K, Y, Z, X, a, d, f, i, b, h, l, m, c, k, y, z, x
- STE · Stearic acid · ligand · 35 copies · chains B, m, t, H, a, C, I, J, L, M, l, R, A, T, b, D, X, Z, d, c, k, x, h, j
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, D, F, J, K, Z, Y, T, b, H, X, a, m, c, k, z, i, d, f, j, h, x, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 13 copies · chains A, C, I, D, F, J, B, H, L, M, K, Y, a, i, o, b, c, k, y, d, f, j, l, m
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, D, E, L, T, C, B, M, a, b, d, l, m, t, c, e, j
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains A, C, D, J, K, T, B, L, l, t, F, X, a, c, d, j, k, M, b, f, x
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 4 copies · chains A, D, F, L, T, a, d, f, x, l, t
- OEY · Ca-MN4-O6 cluster · ligand · 2 copies · chains A, C, a, c
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, R, e, f, r
- HEC · Heme C · ligand · 2 copies · chains V, v
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · 9 copies · chains A, I, O, b, C, J, D, V, B, H, a, c, j, d, v, h
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- Q8DIF8 · AlphaFold monomer V2.0 prediction for photosystem II CP43 reaction center protein (Q8DIF8) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P0A444 · AlphaFold monomer V2.0 prediction for photosystem II protein D1 1 (P0A444) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P0A431 · AlphaFold monomer V2.0 prediction for photosystem II manganese- stabilizing polypeptide… · a predicted model of the same protein · chain O against A, TM-score 1.00
- P0A386 · AlphaFold monomer V2.0 prediction for cytochrome C-550 (P0A386) · a predicted model of the same protein · chain V against A, TM-score 1.00
- Q8DHJ2 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein Z (Q8DHJ2) · a predicted model of the same protein · chain Z against A, TM-score 0.91
- Q9F1K9 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein K (Q9F1K9) · a predicted model of the same protein · chain K against A, TM-score 0.88
- Q8DIN8 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein L (Q8DIN8) · a predicted model of the same protein · chain l against A, TM-score 0.86
- Q9F1R6 · AlphaFold monomer V2.0 prediction for photosystem II reaction center X protein (Q9F1R6) · a predicted model of the same protein · chain X against A, TM-score 0.85
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 P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DKM3
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 7RF5 · PDBe 7RF5 · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DKM3 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q9F1R6 · UniProt Q8DJI1 · UniProt Q8DHJ2
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