Research workbench
Cryo-EM structure of psii intermediate PSB28-psii complex
Analyse Cryo-EM structure of psii intermediate PSB28-psii complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DXH
- Type
- protein
- Length
- 2,150 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II reaction center PSB28 protein; TSL0063 protein; Photosystem II protein D1…
- UniProt
- Q8DLJ8, Q8DMP8, P51765, D0VWR1, D0VWR8, P12238, P12239, P19052, P12240, P12241, P12312, P12313, D0VWR4, D0VWR7, Q9F1K9, D0VWR5, D0VWR3
- Ligands
- CLA, BCR, MGE, DGD, SQD, PHO, UNL, PQ9, HEM, FE2, CL
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 18 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II reaction center PSB28 protein | protein | 109 | 19% helix, 32% strand | Q8DLJ8 |
| B | TSL0063 protein | protein | 48 | 56% helix, 4% strand | Q8DMP8 |
| a | Photosystem II protein D1 | protein | 297 | 59% helix, 4% strand | P51765 |
| b | Photosystem II CP47 reaction center protein | protein | 494 | 45% helix, 10% strand | D0VWR1 |
| d | Photosystem II D2 protein | protein | 339 | 59% helix, 2% strand | D0VWR8 |
| e | Cytochrome B559 subunit alpha | protein | 63 | 38% helix, 0% strand | P12238 |
| f | Cytochrome B559 subunit beta | protein | 28 | 61% helix, 0% strand | P12239 |
| h | Photosystem II reaction center protein H | protein | 62 | 44% helix, 10% strand | P19052 |
| i | Photosystem II reaction center protein I | protein | 29 | 79% helix, 0% strand | P12240 |
| l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | P12241 |
| m | Photosystem II reaction center protein M | protein | 31 | 68% helix, 0% strand | P12312 |
| t | Photosystem II reaction center protein T | protein | 27 | 78% helix, 0% strand | P12313 |
| x | Photosystem II reaction center protein X | protein | 36 | 83% helix, 0% strand | D0VWR4 |
| c | Photosystem II CP43 reaction center protein | protein | 403 | 47% helix, 3% strand | D0VWR7 |
| k | Photosystem II reaction center protein K | protein | 34 | 47% helix, 0% strand | Q9F1K9 |
| z | Photosystem II reaction center protein Z | protein | 62 | 40% helix, 0% strand | D0VWR5 |
| y | Photosystem II reaction center protein YCF12 | protein | 28 | 39% helix, 0% strand | D0VWR3 |
| C | Unidentified transmembrane protein | protein | 23 | 78% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 34 copies · chains a, d, t, i, b, h, l, m, B, x, c, k, z
- BCR · Beta-carotene · ligand · 9 copies · chains a, i, b, m, d, f, h, x, c, k, z
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · ligand · 7 copies · chains B, b, d, l, m, a, t, f, i, c
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 4 copies · chains a, d, c, b, h
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains a, t, l, m
- PHO · Pheophytin A · ligand · 2 copies · chains a, d
- UNL · Unknown ligand · ligand · 2 copies · chains b, d, h, x
- 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 · ligand · chains a, d, l
- HEM · Protoporphyrin IX containing Fe · ligand · chains e, f
- FE2 · Fe (II) ion · metal · chains a, d
- CL · Chloride ion · ion · 2 copies · chains a, d, c
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains a, d, b, m, t
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · chains 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 | 952 | 0.83 | 0.84 | 72 | BCR, CLA |
| 2 | 993 | 0.81 | 0.82 | 62 | CLA |
| 3 | 1157 | 0.81 | 0.82 | 113 | CLA, DGD |
| 4 | 1149 | 0.78 | 0.80 | 114 | CL |
| 5 | 1183 | 0.77 | 0.79 | 106 | CLA, DGD |
Interfaces
44 interfaces between chains.
- a–d · 4738 Ų buried · 33 hydrogen bonds · protein-protein
- b–d · 2554 Ų buried · 26 hydrogen bonds · protein-protein
- b–h · 1829 Ų buried · 23 hydrogen bonds · protein-protein
- B–b · 1581 Ų buried · 7 hydrogen bonds · protein-protein
- a–c · 1579 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 7DXH · Cryo-EM structure of PSII intermediate Psb28-PSII complex · the same entry in another collection · chain m against m, 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 Q8DLJ8
- Every structure of UniProt Q8DMP8
- Every structure of UniProt P51765
- Every structure of UniProt D0VWR1
- 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 P12241
- Every structure of UniProt P12312
- Every structure of UniProt P12313
- Every structure of UniProt D0VWR4
- Every structure of UniProt D0VWR7
- Every structure of UniProt Q9F1K9
- Every structure of UniProt D0VWR5
- Every structure of UniProt D0VWR3
- Elsewhere: RCSB PDB 7DXH · PDBe 7DXH · UniProt Q8DLJ8 · UniProt Q8DMP8 · UniProt P51765 · UniProt D0VWR1 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt P12241 · UniProt P12312 · UniProt P12313 · UniProt D0VWR4 · UniProt D0VWR7 · UniProt Q9F1K9 · UniProt D0VWR5 · UniProt D0VWR3
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