MolNFT v1 · #17047 · protein
Lipidic cubic phase crystal structure of the photosynthetic reaction centre from rhodobacter sphaeroides
1OGV · Reaction center protein H chain: “Lipidic cubic phase crystal structure of the photosynthetic reaction centre from rhodobacter sphaeroides”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 10 pockets (best druggability 0.82). MolNFT…
- PDB
- 1OGV
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- BCL, BPH, U10, CDL, FE2, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 237 | 24% helix, 24% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 281 | 62% helix, 3% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 301 | 64% helix, 3% strand | P0C0Y9 |
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 · chains L, M
- CDL · Cardiolipin · ligand · chains H, L, M
- FE2 · Fe (II) ion · metal · chains L, M
- CL · Chloride ion · ion · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.82 | 0.84 | 70 | BCL |
| 2 | 70 | 0.71 | 0.96 | 28 | empty |
| 3 | 72 | 0.71 | 0.95 | 17 | empty |
| 4 | 209 | 0.69 | 0.86 | 29 | U10 |
| 5 | 103 | 0.62 | 0.87 | 26 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4585 Ų buried · 74 hydrogen bonds · protein-protein
- H–M · 2863 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1604 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1OGV · Lipidic cubic phase crystal structure of the photosynthetic reaction centre from… · the same entry in another collection · chain H against H, 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
- 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 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 1OGV · PDBe 1OGV · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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