Research workbench
XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 200-nanosecond delay
Analyse XFEL structure of cyanobacterial photosystem II following two flashes (2F) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8IRE
- Type
- protein
- Length
- 5,289 residues
- Chains
- 39
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Thermostichus vulcanus
- Molecule
- Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P51765, D0VWR1, D0VWR7, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P19054, P12241, P12312, D0VWR2, P12313, P56152, P0A387, D0VWR4, D0VWR3, D0VWR5, P0DM37
- Ligands
- CLA, BCR, UNL, LMG, LHG, SQD, PHO, PL9, OEX, BCT, HEM, HEC, DGD, CA, FE2, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.25 · 27 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P51765 |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 51% helix, 11% strand | D0VWR1 |
| C | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 6% strand | D0VWR7 |
| D | Photosystem II D2 protein | protein | 342 | 64% helix, 3% strand | D0VWR8 |
| E | Cytochrome b559 subunit alpha | protein | 81 | 54% helix, 0% strand | P12238 |
| F | Cytochrome b559 subunit beta | protein | 34 | 68% helix, 0% strand | P12239 |
| H, h | Photosystem II reaction center protein H | protein | 64 | 55% helix, 3% strand | P19052 |
| I, i | Photosystem II reaction center protein I | protein | 38 | 68% helix, 0% strand | P12240 |
| J | Photosystem II reaction center protein J | protein | 38 | 58% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | P19054 |
| L, l | Photosystem II reaction center protein L | protein | 36 | 64% helix, 3% strand | P12241 |
| M | Photosystem II reaction center protein M | protein | 33 | 76% helix, 0% strand | P12312 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 47% strand | D0VWR2 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| U | Photosystem II 12 kDa extrinsic protein | protein | 96 | 50% helix, 4% strand | P56152 |
| V, v | Cytochrome c-550 | protein | 137 | 49% helix, 6% strand | P0A387 |
| X, x | Photosystem II reaction center protein X | protein | 38 | 79% helix, 0% strand | D0VWR4 |
| Y, y | Photosystem II reaction center protein Ycf12 | protein | 29 | 79% helix, 0% strand | D0VWR3 |
| c | Photosystem II CP43 reaction center protein | protein | 455 | 56% helix, 6% strand | D0VWR7 |
| d | Photosystem II D2 protein | protein | 341 | 66% helix, 4% strand | D0VWR8 |
| e | Cytochrome b559 subunit alpha | protein | 79 | 56% helix, 0% strand | P12238 |
| f | Cytochrome b559 subunit beta | protein | 31 | 74% helix, 0% strand | P12239 |
| j | Photosystem II reaction center protein J | protein | 39 | 56% helix, 0% strand | Q7DGD4 |
| m | Photosystem II reaction center protein M | protein | 34 | 74% helix, 0% strand | P12312 |
| u | Photosystem II 12 kDa extrinsic protein | protein | 97 | 52% helix, 4% strand | P56152 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | D0VWR5 |
| R | Photosystem II protein Y | protein | 34 | 91% helix, 0% strand | P0DM37 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, I, B, H, M, t, C, K, Y, Z, X, a, d, l, i, b, h, m, c, k, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, T, b, Y, a, i, m, c, k, z, d, f, j, h, x, y
- UNL · Unknown ligand · ligand · 18 copies · chains A, B, D, H, X, I, J, C, K, M, l, a, b, c, d, k, h, x, i, j, m
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains B, D, L, M, A, C, I, J, K, Y, Z, F, a, c, i, j, k, y, z, d, f, b, l, m
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, B, D, L, M, T, C, E, F, a, d, l, t, c, b, m, e, f
- 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, h, B, L, l, m, t, E, F, X, R, a, c, d, k, M, e, 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, X, L, T, a, d, f, x, l, t
- 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
- HEC · Heme C · ligand · 2 copies · chains C, V, c, v
- DGD · Digalactosyl diacyl glycerol (dgdg) · sugar · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
- CA · Calcium ion · metal · 7 copies · chains C, F, V, O, c, a, f, v, o
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- MG · Magnesium ion · metal · 2 copies · chains F, J, f, j
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
- GOL · Glycerol · additive · 21 copies · chains A, b, D, L, M, T, B, H, C, V, O, U, a, d, m, t, l, h, c, v, o, u
- LMT · Dodecyl-beta-D-maltoside · additive · 14 copies · chains A, D, O, b, B, H, X, E, F, J, C, I, M, l, m, T, a, d, c, i, h, e, f, j, L, t
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 11 copies · chains B, a, o, O, C, D, H, V, A, b, c, d, 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 | 982 | 0.87 | 0.87 | 77 | CLA, BCR |
| 2 | 966 | 0.87 | 0.87 | 80 | CLA, BCR |
| 3 | 970 | 0.86 | 0.87 | 80 | HEC |
| 4 | 1015 | 0.85 | 0.85 | 83 | HEC |
| 5 | 204 | 0.83 | 0.96 | 35 | GOL |
Interfaces
132 interfaces between chains.
- a–d · 5488 Ų buried · 61 hydrogen bonds · protein-protein
- A–D · 5461 Ų buried · 69 hydrogen bonds · protein-protein
- a–c · 3269 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 3268 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 3035 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide).
Compared structures
- D0VWR1 · AlphaFold monomer V2.0 prediction for photosystem II CP47 reaction center protein (D0VWR1) · a predicted model of the same protein · chain B against A, TM-score 1.00
- D0VWR8 · AlphaFold monomer V2.0 prediction for photosystem II D2 protein (D0VWR8) · a predicted model of the same protein · chain d against A, TM-score 1.00
- P51765 · AlphaFold monomer V2.0 prediction for photosystem II protein D1 (P51765) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P56152 · AlphaFold monomer V2.0 prediction for photosystem II 12 kda extrinsic protein (P56152) · a predicted model of the same protein · chain U against A, TM-score 0.99
- D0VWR7 · AlphaFold monomer V2.0 prediction for photosystem II CP43 reaction center protein (D0VWR7) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P0A387 · AlphaFold monomer V2.0 prediction for cytochrome C-550 (P0A387) · a predicted model of the same protein · chain V against A, TM-score 0.98
- D0VWR2 · AlphaFold monomer V2.0 prediction for photosystem II manganese- stabilizing polypeptide… · a predicted model of the same protein · chain O against A, TM-score 0.98
- D0VWR5 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein Z (D0VWR5) · a predicted model of the same protein · chain Z against A, TM-score 0.96
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 P51765
- Every structure of UniProt D0VWR1
- Every structure of UniProt D0VWR7
- Every structure of UniProt D0VWR8
- Every structure of UniProt P12238
- Every structure of UniProt P12239
- Every structure of UniProt P19052
- Every structure of UniProt P12240
- Every structure of UniProt Q7DGD4
- Every structure of UniProt P19054
- Every structure of UniProt P12241
- Every structure of UniProt P12312
- Every structure of UniProt D0VWR2
- Every structure of UniProt P12313
- Every structure of UniProt P56152
- Every structure of UniProt P0A387
- Every structure of UniProt D0VWR4
- Every structure of UniProt D0VWR3
- Every structure of UniProt D0VWR5
- Every structure of UniProt P0DM37
- Elsewhere: RCSB PDB 8IRE · PDBe 8IRE · UniProt P51765 · UniProt D0VWR1 · UniProt D0VWR7 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt Q7DGD4 · UniProt P19054 · UniProt P12241 · UniProt P12312 · UniProt D0VWR2 · UniProt P12313 · UniProt P56152 · UniProt P0A387 · UniProt D0VWR4 · UniProt D0VWR3 · UniProt D0VWR5 · UniProt P0DM37
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