Research workbench
Crystal structure of Lsd18 (a flavin-dependent monooxygenase)
Analyse Crystal structure of Lsd18 (a flavin-dependent monooxygenase) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8UP4
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.51
- Source
- Streptomyces lasalocidi
- Molecule
- Flavin-dependent monooxygenase Lsd18
- UniProt
- B5M9L6
- Ligands
- FAD, CL
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.51 · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Flavin-dependent monooxygenase Lsd18 | protein | 468 | 37% helix, 24% strand | B5M9L6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.87 | 0.88 | 117 | FAD, CL |
| 2 | 502 | 0.84 | 0.90 | 45 | empty |
| 3 | 411 | 0.78 | 0.87 | 56 | FAD, CL |
| 4 | 167 | 0.52 | 0.79 | 28 | empty |
| 5 | 144 | 0.51 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 469 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- B5M9L6 · AlphaFold monomer V2.0 prediction for putative epoxidase lasc (B5M9L6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 B5M9L6
- Elsewhere: RCSB PDB 8UP4 · PDBe 8UP4 · UniProt B5M9L6
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