MolNFT v1 · #28918 · protein
Structure of the photochemical reaction center of a spheroidene containing purple bacterium, rhodobacter sphaeroides Y, at 3 ångströms resolution
1YST · Photosynthetic reaction center (L subunit): “Structure of the photochemical reaction center of a spheroidene containing purple bacterium, rhodobacter…”. X-ray diffraction, 5 ligands (BCL, BPH, U10), 15 pockets (best druggability…
- PDB
- 1YST
- Type
- protein
- Length
- 838 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center (L subunit); Photosynthetic reaction center (M subunit)…
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, BPH, U10, SPO, MN
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Photosynthetic reaction center (L subunit) | protein | 273 | 54% helix, 1% strand | P02954 |
| M | Photosynthetic reaction center (M subunit) | protein | 305 | 56% helix, 2% strand | P02953 |
| H | Photosynthetic reaction center (H subunit) | protein | 260 | 16% helix, 17% strand | P11846 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, H
- SPO · Spheroidene · ligand · chains M
- MN · Manganese (II) ion · metal · chains L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.79 | 0.84 | 56 | BCL |
| 2 | 455 | 0.68 | 0.80 | 51 | empty |
| 3 | 199 | 0.66 | 0.84 | 22 | empty |
| 4 | 207 | 0.64 | 0.84 | 33 | empty |
| 5 | 89 | 0.57 | 0.86 | 19 | SPO |
Interfaces
3 interfaces between chains.
- L–M · 4549 Ų buried · 44 hydrogen bonds · protein-protein
- M–H · 2904 Ų buried · 33 hydrogen bonds · protein-protein
- L–H · 1665 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1YST · Structure of the photochemical reaction center of a spheroidene containing purple… · the same entry in another collection · chain L against L, 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 P02954
- Every structure of UniProt P02953
- Every structure of UniProt P11846
- Elsewhere: RCSB PDB 1YST · PDBe 1YST · UniProt P02954 · UniProt P02953 · UniProt P11846
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