MolNFT v1 · #27065 · protein
Crystal structure of retinol dehydratase in complex with anhydroretinol and inactive cofactor pap
1X8K: “Crystal structure of retinol dehydratase in complex with anhydroretinol and inactive cofactor pap”. X-ray diffraction, 4 ligands (EMC, ANR, A3P), 2 pockets (best druggability 0.87). MolNFT v1 #27065 on GenesisL1: 3D structure…
- PDB
- 1X8K
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol dehydratase
- UniProt
- Q26490
- Ligands
- EMC, ANR, A3P, CA
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol dehydratase | protein | 344 | 50% helix, 9% strand | Q26490 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 2 copies · chains A, B
- ANR · Anhydroretinol · ligand · 2 copies · chains A, B
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.87 | 0.90 | 84 | A3P, ANR |
| 2 | 717 | 0.86 | 0.90 | 76 | ANR, A3P |
Interfaces
1 interface between chains.
- A–B · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1X8K · Crystal structure of retinol dehydratase in complex with anhydroretinol and inactive… · the same entry in another collection · 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 Q26490
- Elsewhere: RCSB PDB 1X8K · PDBe 1X8K · UniProt Q26490
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