Research workbench
Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8
Analyse Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SU3
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 48C12 heliorhodopsin
- Ligands
- LFA, RET, OLA, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 48C12 heliorhodopsin | protein | 256 | 73% helix, 6% strand | — |
| A | 48C12 heliorhodopsin | protein | 256 | 71% helix, 6% strand | — |
Ligands and binding sites
- LFA · Eicosane · ligand · 26 copies · chains X, A
- RET · Retinal · ligand · 2 copies · chains X, A
- OLA · Oleic acid · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains X
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains X, A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.76 | 0.92 | 25 | LFA, RET |
| 2 | 183 | 0.75 | 0.91 | 32 | LFA, RET |
| 3 | 71 | 0.55 | 0.87 | 21 | empty |
| 4 | 73 | 0.47 | 0.82 | 27 | empty |
| 5 | 105 | 0.37 | 0.74 | 30 | LFA |
Interfaces
1 interface between chains.
- X–A · 2350 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 6SU3 · Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8 · the same entry in another collection · chain X against X, 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
- Elsewhere: RCSB PDB 6SU3 · PDBe 6SU3
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