Research workbench
Psii intermediate PSB28-RC47
Analyse Psii intermediate PSB28-RC47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DXA
- Type
- protein
- Length
- 1,629 residues
- Chains
- 14
- 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
- Ligands
- CLA, MGE, BCR, SQD, PHO, UNL, PQ9, DGD, HEM, FE2, CL
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 14 distinct chains · 52% helix, 7% 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 | 50 | 56% helix, 4% strand | Q8DMP8 |
| a | Photosystem II protein D1 | protein | 298 | 58% helix, 6% strand | P51765 |
| b | Photosystem II CP47 reaction center protein | protein | 494 | 46% helix, 11% strand | D0VWR1 |
| d | Photosystem II D2 protein | protein | 339 | 58% helix, 3% strand | D0VWR8 |
| e | Cytochrome B559 subunit alpha | protein | 63 | 43% helix, 0% strand | P12238 |
| f | Cytochrome B559 subunit beta | protein | 28 | 75% helix, 0% strand | P12239 |
| h | Photosystem II reaction center protein H | protein | 62 | 44% helix, 6% strand | P19052 |
| i | Photosystem II reaction center protein I | protein | 29 | 76% 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 | 84% helix, 0% strand | P12312 |
| t | Photosystem II reaction center protein T | protein | 30 | 63% helix, 0% strand | P12313 |
| x | Photosystem II reaction center protein X | protein | 36 | 83% helix, 0% strand | D0VWR4 |
| C | Unidentified transmembrane protein | protein | 23 | 65% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 22 copies · chains a, d, t, i, b, h, l, m, B, x
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · ligand · 7 copies · chains a, i, b, l, m, B, d, f, t
- BCR · Beta-carotene · ligand · 6 copies · chains a, i, b, m, d, f, h, x
- 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
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains b, d, h
- HEM · Protoporphyrin IX containing Fe · ligand · chains e, f
- FE2 · Fe (II) ion · metal · chains a, d
- CL · Chloride ion · ion · chains a, d
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains b, m, a, d, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.84 | 0.84 | 107 | MGE |
| 2 | 1045 | 0.80 | 0.81 | 98 | CLA, DGD |
| 3 | 681 | 0.80 | 0.84 | 63 | CLA |
| 4 | 982 | 0.76 | 0.78 | 81 | CL |
| 5 | 257 | 0.63 | 0.80 | 33 | empty |
Interfaces
38 interfaces between chains.
- a–d · 4791 Ų buried · 40 hydrogen bonds · protein-protein
- b–d · 2569 Ų buried · 26 hydrogen bonds · protein-protein
- b–h · 1836 Ų buried · 25 hydrogen bonds · protein-protein
- B–b · 1567 Ų buried · 9 hydrogen bonds · protein-protein
- d–e · 1245 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7DXA · PSII intermediate Psb28-RC47 · 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
- Elsewhere: RCSB PDB 7DXA · PDBe 7DXA · 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
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