MolNFT v1 · #106432 · protein
Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form
4RYX · Retinoid isomerohydrolase: “Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form”. X-ray diffraction, 4 ligands (PLM, A3V, FE2), 3 pockets (best druggability 0.86). MolNFT v1 #106432 on GenesisL1…
- PDB
- 4RYX
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoid isomerohydrolase
- EC
- 3.1.1.64
- UniProt
- Q28175
- Ligands
- PLM, A3V, FE2, SO4
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoid isomerohydrolase (EC 3.1.1.64) | protein | 510 | 10% helix, 45% strand | Q28175 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- A3V · (1R)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.86 | 0.92 | 65 | PLM, A3V |
| 2 | 581 | 0.78 | 0.84 | 52 | empty |
| 3 | 151 | 0.44 | 0.75 | 21 | empty |
Compared structures
- 4RYX · Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form · the same entry in another collection · chain A against A, TM-score 1.00
- Q28175 · AlphaFold monomer V2.0 prediction for retinoid isomerohydrolase (Q28175) · a predicted model of the same protein · chain A against A, 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
- Every structure of UniProt Q28175
- Elsewhere: RCSB PDB 4RYX · PDBe 4RYX · UniProt Q28175
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