MolNFT v1 · #51102 · protein
X-ray high resolution structure of the photosynthetic reaction center from rb. sphaeroides at pH 10 in the charge-separated state, 2ND dataset
2UXM · Reaction center protein H chain: “X-ray high resolution structure of the photosynthetic reaction center from rb. sphaeroides at pH 10 in the…”. X-ray diffraction, 8 ligands (BCL, BPH, UQ2), 16 pockets (best druggability 0.83).…
- PDB
- 2UXM
- Type
- protein
- Length
- 823 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, UQ2, HTO, U10, SPO, FE, PO4
- Pockets
- 16 · best druggability 0.83
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 | 240 | 25% helix, 24% 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, M
- HTO · Heptane-1,2,3-triol · ligand · chains L
- U10 · Ubiquinone-10 · ligand · chains L, M
- SPO · Spheroidene · ligand · chains 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 · 4 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.83 | 0.85 | 68 | BCL |
| 2 | 126 | 0.77 | 0.96 | 32 | empty |
| 3 | 64 | 0.70 | 0.96 | 18 | empty |
| 4 | 177 | 0.69 | 0.87 | 31 | U10 |
| 5 | 142 | 0.60 | 0.84 | 25 | UQ2 |
Interfaces
3 interfaces between chains.
- L–M · 4535 Ų buried · 71 hydrogen bonds · protein-protein
- H–M · 2842 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 1611 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2UXM · 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
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 2UXM · PDBe 2UXM · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.