Research workbench
Crystal structure of RPE65 in complex with mb-004 and palmitate
Analyse Crystal structure of RPE65 in complex with mb-004 and palmitate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UL5
- Type
- protein
- Length
- 1,024 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
- PLM, 8D7, FE2, NA
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoid isomerohydrolase (EC 3.1.1.64) | protein | 511 | 11% helix, 44% strand | Q28175 |
| B | Retinoid isomerohydrolase (EC 3.1.1.64) | protein | 513 | 11% helix, 43% strand | Q28175 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- 8D7 · (1R)-3-amino-1-{3-[(2-propylpentyl)oxy]phenyl}propan-1-ol · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.86 | 0.93 | 62 | PLM, 8D7 |
| 2 | 417 | 0.85 | 0.93 | 67 | PLM, 8D7 |
| 3 | 410 | 0.79 | 0.88 | 44 | empty |
| 4 | 460 | 0.79 | 0.87 | 49 | empty |
| 5 | 254 | 0.56 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1617 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5UL5 · Crystal structure of RPE65 in complex with MB-004 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 5UL5 · PDBe 5UL5 · UniProt Q28175
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