MolNFT v1 · #106434 · protein
Crystal structure of RPE65 in complex with S-emixustat and palmitate
4RYZ · Retinoid isomerohydrolase: “Crystal structure of RPE65 in complex with S-emixustat and palmitate”. X-ray diffraction, 4 ligands (ACE, PLM, A5V), 10 pockets (best druggability 0.84). MolNFT v1 #106434 on GenesisL1: 3D structure…
- PDB
- 4RYZ
- Type
- protein
- Length
- 1,020 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoid isomerohydrolase
- EC
- 3.1.1.64
- UniProt
- Q28175
- Ligands
- ACE, PLM, A5V, FE2
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinoid isomerohydrolase (EC 3.1.1.64) | protein | 510 | 11% helix, 44% strand | Q28175 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- A5V · (1S)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.84 | 0.90 | 71 | PLM, A5V |
| 2 | 437 | 0.84 | 0.91 | 69 | PLM, A5V |
| 3 | 437 | 0.80 | 0.88 | 45 | empty |
| 4 | 440 | 0.79 | 0.87 | 44 | empty |
| 5 | 344 | 0.58 | 0.76 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1624 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4RYZ · Crystal structure of RPE65 in complex with S-emixustat and palmitate · 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 0.99
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 4RYZ · PDBe 4RYZ · UniProt Q28175
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