MolNFT v1 · #179525 · protein
Crystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl ether
7K88 · Retinoid isomerohydrolase: “Crystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl ether”. X-ray diffraction, 4 ligands (ACE, 32M, FE2), 9 pockets (best druggability 0.83). MolNFT v1 #179525 on GenesisL1: 3D…
- PDB
- 7K88
- Type
- protein
- Length
- 1,004 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, 32M, FE2, NA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoid isomerohydrolase (EC 3.1.1.64, 5.3.3.22) | protein | 501 | 9% helix, 45% strand | Q28175 |
| B | Retinoid isomerohydrolase (EC 3.1.1.64, 5.3.3.22) | protein | 503 | 9% helix, 44% strand | Q28175 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- 32M · 3,6,9,12,15,18-hexaoxahexacosan-1-ol · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PG4 · Tetraethylene glycol · additive · chains 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 | 465 | 0.83 | 0.90 | 63 | 32M |
| 2 | 528 | 0.82 | 0.87 | 74 | 32M |
| 3 | 436 | 0.80 | 0.88 | 44 | empty |
| 4 | 521 | 0.78 | 0.85 | 53 | empty |
| 5 | 260 | 0.55 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K88 · Crystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl ether · 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 7K88 · PDBe 7K88 · UniProt Q28175
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