Research workbench
Crystal structure of bovine RPE65 in complex with 4-fluoro-mb-004 and palmitate
Analyse Crystal structure of bovine RPE65 in complex with 4-fluoro-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
- 7K8G
- Type
- protein
- Length
- 1,001 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
- PLM, W9A, FE2
- Pockets
- 6 · best druggability 0.81
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 | 499 | 9% helix, 45% strand | Q28175 |
| B | Retinoid isomerohydrolase (EC 3.1.1.64, 5.3.3.22) | protein | 502 | 9% helix, 45% strand | Q28175 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- W9A · (1R)-3-amino-1-{4-fluoro-3-[(2-propylpentyl) oxy]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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.81 | 0.88 | 66 | PLM, W9A |
| 2 | 525 | 0.81 | 0.87 | 69 | PLM, W9A |
| 3 | 612 | 0.79 | 0.85 | 60 | empty |
| 4 | 511 | 0.79 | 0.86 | 51 | empty |
| 5 | 389 | 0.57 | 0.75 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7K8G · Crystal structure of bovine RPE65 in complex with 4-fluoro-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 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 7K8G · PDBe 7K8G · UniProt Q28175
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