MolNFT v1 · #110865 · protein
The 1.43 ångström crystal structure of bacteriorhodopsin crystallized from bicelles
4Y9H: “The 1.43 ångström crystal structure of bacteriorhodopsin crystallized from bicelles”. X-ray diffraction, 6 ligands (D12, D10, RET), 1 pocket (best druggability 0.80). MolNFT v1 #110865 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Y9H
- Type
- protein
- Length
- 226 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- B0R5N9
- Ligands
- D12, D10, RET, HP6, R16, PO4
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 226 | 78% helix, 5% strand | B0R5N9 |
Ligands and binding sites
- D12 · Dodecane · ligand · 8 copies · chains A
- D10 · Decane · ligand · 4 copies · chains A
- RET · Retinal · ligand · chains A
- HP6 · Heptane · ligand
- R16 · Hexadecane · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- DD9 · nonane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.80 | 0.98 | 20 | RET |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 4Y9H · The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles · the same entry in another collection · chain A against A, 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 B0R5N9
- Elsewhere: RCSB PDB 4Y9H · PDBe 4Y9H · UniProt B0R5N9
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