Research workbench
Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin
Analyse Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VHZ
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- SGA, RET, SOG, L2P, GLC, MAN
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 228 | 76% helix, 4% strand | P02945 |
Ligands and binding sites
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · chains A
- RET · Retinal · ligand · chains A
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · chains A
- L2P · 2,3-di-phytanyl-glycerol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · 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 | 161 | 0.82 | 0.97 | 38 | RET |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 3VHZ · Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin · 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 0.99
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 3VHZ · PDBe 3VHZ · UniProt P02945
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