UniProt D0VWR8
Photosystem II D2 protein (D0VWR8)
Photosystem II D2 protein (UniProt D0VWR8), EC 1.10.3.9: 58 experimental structures and 1 predicted model on GenesisL1, 14 ligands bound, 357 pockets. Binding sites, druggability and experiment against prediction (TM-score) in…
- UniProt
- D0VWR8
- Protein
- Photosystem II D2 protein
- EC
- 1.10.3.9
- Experimental structures
- 58
- Predicted models
- 1
- Ligands
- 14
- Pockets
- 357 · 29 records with a druggable one
Structures
59 records of D0VWR8 in the MolNFT archive: 58 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3WU2 | Crystal structure analysis of Photosystem II complex | x-ray diffraction | D, d | — | — |
| 3WU2 | Crystal structure analysis of photosystem II complex | x-ray diffraction | D, d | — | — |
| 4UB6 | Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | x-ray diffraction | D, d | — | — |
| 4UB6 | Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | x-ray diffraction | D, d | — | — |
| 4UB8 | Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | x-ray diffraction | D, d | — | — |
| 4UB8 | Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | x-ray diffraction | D, d | — | — |
| 5B5E | Crystal structure analysis of photosystem II complex | x-ray diffraction | D, d | — | — |
| 5B66 | Crystal structure analysis of photosystem II complex | x-ray diffraction | D, d | — | — |
| 5GTH | Native XFEL structure of photosystem II (dark dataset) | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 5GTH | Native xfel structure of photosystem II (dark dataset) | x-ray diffraction | D, d | — | — |
| 5GTI | Native XFEL structure of photosystem II (two flash dataset) | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.82) |
| 5GTI | Native xfel structure of photosystem II (two flash dataset) | x-ray diffraction | D, d | — | — |
| 5V2C | Re-refinement of crystal structure of photosystem II complex | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, PL9 | 13 (best 0.83) |
| 5V2C | Re-refinement of crystal structure of photosystem II complex | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, PL9 | — |
| 5WS5 | Native XFEL structure of photosystem II (preflash dark dataset) | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.83) |
| 5WS5 | Native xfel structure of photosystem II (preflash dark dataset) | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | — |
| 5WS6 | Native xfel structure of photosystem II (preflash two-flash dataset | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLJ | Xfel structure of cyanobacterial photosystem II (dark state, DATASET1) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLK | XFEL structure of cyanobacterial photosystem II (1F state, dataset1) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | 13 (best 0.84) |
| 6JLK | Xfel structure of cyanobacterial photosystem II (1F state, DATASET1) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLL | XFEL structure of cyanobacterial photosystem II (2F state, dataset1) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | 13 (best 0.83) |
| 6JLL | Xfel structure of cyanobacterial photosystem II (2F state, DATASET1) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLM | XFEL structure of cyanobacterial photosystem II (dark state, dataset2) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | 13 (best 0.83) |
| 6JLM | Xfel structure of cyanobacterial photosystem II (dark state, DATASET2) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLN | XFEL structure of cyanobacterial photosystem II (1F state, dataset2) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | 14 (best 0.83) |
| 6JLN | Xfel structure of cyanobacterial photosystem II (1F state, DATASET2) | x-ray diffraction | D, d | FE2, CL, BCT, CLA, PHO, SQD | — |
| 6JLO | Xfel structure of cyanobacterial photosystem II (2F state, DATASET2) | x-ray diffraction | D, d | CL, BCT, CLA, PHO, SQD, PL9 | — |
| 6JLP | XFEL structure of cyanobacterial photosystem II (3F state, dataset2) | x-ray diffraction | D, d | FE2, CL, CLA, SQD, PL9, DGD | 13 (best 0.83) |
| 6JLP | Xfel structure of cyanobacterial photosystem II (3F state, DATASET2) | x-ray diffraction | D, d | FE2, CL, CLA, SQD, PL9, DGD | — |
| 7CJI | Photosystem II structure in the S1 state | x-ray diffraction | D, d | FE2, CL, CLA, PHO, PL9, LHG | — |
| 7CJJ | Photosystem II structure in the S2 state | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.83) |
| 7CJJ | Photosystem II structure in the S2 state | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | — |
| 7COU | Structure of cyanobacterial photosystem II in the dark S1 state | x-ray diffraction | D, d | FE2, CL, CLA, PHO, PL9, LHG | 13 (best 0.82) |
| 7COU | Structure of cyanobacterial photosystem II in the dark S1 state | x-ray diffraction | D, d | FE2, CL, CLA, PHO, PL9, LHG | — |
| 7CZL | Structural insights into a dimeric PSB27-photosystem II complex from a cyanobacterium… | electron microscopy | D, d | CLA, PHO, PQ9, LHG, BCT, MGE | — |
| 7D1T | Cryo-EM Structure of PSII at 1.95 angstrom resolution | electron microscopy | D, d | FE2, CL, CLA, PHO, SQD, PL9 | — |
| 7D1T | Cryo-EM structure of psii at 1.95 ångström resolution | electron microscopy | D, d | FE2, CL, CLA, PHO, SQD, PL9 | — |
| 7D1U | Cryo-EM structure of psii at 2.08 ångström resolution | electron microscopy | D, d | FE2, CL, CLA, PHO, SQD, PL9 | — |
| 7DXA | PSII intermediate Psb28-RC47 | electron microscopy | d | CLA, PHO, CL, UNL, MGE, FE2 | 13 (best 0.84) |
| 7DXA | Psii intermediate PSB28-RC47 | electron microscopy | d | CLA, PHO, CL, UNL, MGE, FE2 | — |
| 7DXH | Cryo-EM structure of PSII intermediate Psb28-PSII complex | electron microscopy | d | MGE, CLA, CL, DGD, PHO, FE2 | 11 (best 0.81) |
| 7DXH | Cryo-EM structure of psii intermediate PSB28-psii complex | electron microscopy | d | MGE, CLA, CL, DGD, PHO, FE2 | — |
| 7EDA | Structure of monomeric photosystem II | electron microscopy | D | FE2, CLA, PHO, SQD, PL9, DGD | 12 (best 0.81) |
| 7EDA | Structure of monomeric photosystem II | electron microscopy | D | FE2, CLA, PHO, SQD, PL9, DGD | — |
| 8GN1 | Crystal structure of DBBQ-bound photosystem II complex | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 14 (best 0.83) |
| 8GN2 | Crystal structure of PPBQ-bound photosystem II complex | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.83) |
| 8IR5 | XFEL structure of cyanobacterial photosystem II under dark conditions | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.84) |
| 8IR6 | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 20-nanosecond delay | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IR7 | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 200-nanosecond delay | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.83) |
| 8IR8 | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 1-microsecond delay | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IR9 | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 30-microsecond delay | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 13 (best 0.83) |
| 8IRA | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 200-microsecond… | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.82) |
| 8IRB | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IRC | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay… | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IRD | XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 20-nanosecond… | x-ray diffraction | D, d | FE2, CL, CLA, SQD, PL9, BCT | 12 (best 0.83) |
| 8IRE | XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 200-nanosecond… | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IRF | XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 1-microsecond… | x-ray diffraction | D, d | FE2, CL, CLA, PHO, SQD, PL9 | 12 (best 0.83) |
| 8IRI | XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 5-millisecond… | x-ray diffraction | D, d | CL, CLA, PHO, SQD, PL9, LHG | 13 (best 0.83) |
| D0VWR8 | AlphaFold monomer V2.0 prediction for photosystem II D2 protein (D0VWR8) | predicted | A | — | 3 (best 0.60) |
Ligands
- BCR · Beta-carotene · in 48 records
- CLA · Chlorophyll A · in 48 records
- DGD · Digalactosyl diacyl glycerol (dgdg) · in 48 records
- FE2 · Fe (II) ion · in 48 records
- PHO · Pheophytin A · in 48 records
- CL · Chloride ion · in 45 records
- BCT · Bicarbonate ion · in 44 records
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · in 44 records
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · in 44 records
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · in 43 records
- 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 · in 43 records
- UNL · Unknown ligand · in 43 records
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · in 5 records
- PQ9 · 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,22,26-heptaenyl]-2,3-dimethylbenzo-1,4-quinone · in 5 records
Experiment against prediction
- 3WU2 chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.22 Å
- 3WU2 chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.22 Å
- 8GN1 chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.22 Å
- 5V2C chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 5V2C chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 6JLJ chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 6JLK chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 6JLK chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 6JLM chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
- 6JLM chain D against the predicted model D0VWR8: TM-score 1.00, RMSD 0.23 Å
Elsewhere
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