MolNFT v1 · #91846 · protein
Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway
4FPD: “Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway”. X-ray diffraction, 3 ligands (LI1, RET, CL), 2 pockets (best druggability 0.80). MolNFT v1 #91846 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4FPD
- Type
- protein
- Length
- 225 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- LI1, RET, CL
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 225 | 73% helix, 4% strand | P02945 |
Ligands and binding sites
- LI1 · 1-[2,6,10.14-tetramethyl-hexadecan-16-yl]-2-[2,10,14-trimethylhexadecan-16-yl]glycerol · ligand · 8 copies · chains A
- RET · Retinal · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.80 | 0.98 | 25 | RET |
| 2 | 64 | 0.43 | 0.82 | 18 | empty |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 4FPD · Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway · the same entry in another collection · chain A against A, TM-score 1.00
- P02945 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin (P02945) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P02945
- Elsewhere: RCSB PDB 4FPD · PDBe 4FPD · UniProt P02945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.