Research workbench
Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate
Analyse Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K89
- Type
- protein
- Length
- 1,009 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoid isomerohydrolase
- EC
- 3.1.1.64, 5.3.3.22
- UniProt
- Q28175
- Ligands
- ACE, PLM, W4J, FE2, NA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoid isomerohydrolase (EC 3.1.1.64, 5.3.3.22) | protein | 504 | 10% helix, 45% strand | Q28175 |
| B | Retinoid isomerohydrolase (EC 3.1.1.64, 5.3.3.22) | protein | 505 | 9% helix, 45% strand | Q28175 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- W4J · (1R)-3-amino-1-[3-(cyclohexylmethoxy)-4-fluorophenyl]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
- PG4 · Tetraethylene glycol · 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 | 461 | 0.84 | 0.91 | 68 | PLM, W4J |
| 2 | 468 | 0.83 | 0.90 | 70 | PLM, W4J |
| 3 | 517 | 0.79 | 0.86 | 56 | empty |
| 4 | 539 | 0.77 | 0.84 | 53 | empty |
| 5 | 262 | 0.55 | 0.77 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1627 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K89 · Crystal structure of bovine RPE65 in complex with 4-fluoro-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 B 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 7K89 · PDBe 7K89 · UniProt Q28175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.