Research workbench
Halorhodopsin from halobacterium salinarum in a new rhombohedral crystal form
Analyse Halorhodopsin from halobacterium salinarum in a new rhombohedral crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AHY
- Type
- protein
- Length
- 242 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halorhodopsin
- UniProt
- B0R2U4
- Ligands
- RET, CL
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Halorhodopsin | protein | 242 | 78% helix, 3% strand | B0R2U4 |
Ligands and binding sites
- RET · Retinal · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- BOG · octyl beta-D-glucopyranoside · 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 | 122 | 0.79 | 0.97 | 22 | RET |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5AHY · Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form · the same entry in another collection · chain A against A, TM-score 1.00
- B0R2U4 · AlphaFold monomer V2.0 prediction for halorhodopsin (B0R2U4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B0R2U4
- Elsewhere: RCSB PDB 5AHY · PDBe 5AHY · UniProt B0R2U4
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