Research workbench
Crystal structure of mercury derivative of retinol dehydratase in a complex with retinol and pap
Analyse Crystal structure of mercury derivative of retinol dehydratase in a complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FMJ
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol dehydratase
- UniProt
- Q26490
- Ligands
- A3P, RTL, HG, CA
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol dehydratase | protein | 342 | 47% helix, 9% strand | Q26490 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- RTL · Retinol · ligand · 2 copies · chains A, B
- HG · Mercury (II) ion · metal · 6 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.87 | 0.90 | 82 | A3P, RTL |
| 2 | 739 | 0.87 | 0.90 | 84 | A3P, RTL |
| 3 | 141 | 0.39 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 116 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1FMJ · Crystal structure of mercury derivative of retinol dehydratase in a complex with retinol… · 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 1FMJ · PDBe 1FMJ · UniProt Q26490
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