MolNFT v1 · #164324 · protein
Crystal structure of the 48C12 heliorhodopsin in the blue form at pH 4.3
6SU4: “Crystal structure of the 48C12 heliorhodopsin in the blue form at pH 4.3”. X-ray diffraction, 4 ligands (LFA, OLA, RET), 7 pockets (best druggability 0.76). MolNFT v1 #164324 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6SU4
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 48C12 heliorhodopsin
- Ligands
- LFA, OLA, RET, SO4
- Pockets
- 7 · 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 | 254 | 73% helix, 6% strand | — |
| A | 48C12 heliorhodopsin | protein | 254 | 71% helix, 6% strand | — |
Ligands and binding sites
- LFA · Eicosane · ligand · 23 copies · chains X, A
- OLA · Oleic acid · ligand · 3 copies · chains X, A
- RET · Retinal · ligand · 2 copies · chains X, A
- SO4 · Sulfate ion · ion · 2 copies · chains X, A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains X, A
- ACT · Acetate ion · additive · 2 copies · chains X, A
- GOL · Glycerol · additive · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.76 | 0.92 | 27 | RET |
| 2 | 176 | 0.76 | 0.92 | 28 | LFA, RET |
| 3 | 69 | 0.58 | 0.89 | 23 | empty |
| 4 | 85 | 0.56 | 0.86 | 23 | empty |
| 5 | 70 | 0.49 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- X–A · 2389 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 6SU4 · Crystal structure of the 48C12 heliorhodopsin in the blue form at pH 4.3 · 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 6SU4 · PDBe 6SU4
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