MolNFT v1 · #164323 · protein
Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8
6SU3: “Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8”. X-ray diffraction, 4 ligands (LFA, RET, OLA), 6 pockets (best druggability 0.76). MolNFT v1 #164323 on GenesisL1: 3D structure, binding sites and pockets…
- 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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