Research workbench
Bacteriorhodopsin ground state structure obtained with serial femtosecond crystallography
Analyse Bacteriorhodopsin ground state structure obtained with serial femtosecond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7A
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- LI1, RET
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 224 | 75% 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 · 5 copies · chains A
- RET · Retinal · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.80 | 0.97 | 25 | RET |
| 2 | 70 | 0.45 | 0.81 | 16 | empty |
| 3 | 57 | 0.30 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5J7A · Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography · 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 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 P02945
- Elsewhere: RCSB PDB 5J7A · PDBe 5J7A · UniProt P02945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.