Research workbench
X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 9 in the charge-separated state, 2nd dataset
Analyse X-ray high resolution structure of the photosynthetic reaction center from Rb.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UX4
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.51
- Source
- RHODOBACTER SPHAEROIDES
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- BCL, BPH, UQ2, HTO, U10, SPO, CDL, FE, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.51 · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 240 | 25% helix, 25% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 281 | 64% helix, 3% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 63% helix, 4% strand | P0C0Y9 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- UQ2 · Ubiquinone-2 · ligand · chains L
- HTO · Heptane-1,2,3-triol · ligand · chains L
- U10 · Ubiquinone-10 · ligand · chains L, M
- SPO · Spheroidene · ligand · chains M
- CDL · Cardiolipin · ligand · chains H, L, M
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · chains L
- LDA · Lauryl dimethylamine-N-oxide · additive · 9 copies · chains L, M, H
- GOL · Glycerol · additive · 7 copies · chains H, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.82 | 0.83 | 90 | BCL, BPH |
| 2 | 110 | 0.77 | 0.97 | 32 | empty |
| 3 | 58 | 0.69 | 0.96 | 16 | empty |
| 4 | 199 | 0.68 | 0.85 | 31 | U10 |
| 5 | 140 | 0.61 | 0.84 | 29 | UQ2 |
Interfaces
3 interfaces between chains.
- L–M · 4546 Ų buried · 68 hydrogen bonds · protein-protein
- H–M · 2834 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 1604 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2UX4 · X-ray high resolution structure of the photosynthetic reaction center from rb.… · the same entry in another collection · chain H against H, TM-score 1.00
- P0C0Y8 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P0C0Y8) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain M against A, TM-score 0.99
- P0C0Y7 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P0C0Y7) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 P0C0Y7
- Every structure of UniProt P0C0Y8
- Every structure of UniProt P0C0Y9
- Elsewhere: RCSB PDB 2UX4 · PDBe 2UX4 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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