Research workbench
Crystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl ether
Analyse Crystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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