Research workbench
Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form
Analyse Crystal structure of RPE65 in complex with emixustat and palmitate, P6522… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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