Research workbench
Structural basis of histone demethylation by LSD1 revealed by suicide inactivation
Analyse Structural basis of histone demethylation by LSD1 revealed by suicide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UXN
- Type
- protein
- Length
- 804 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1; Rest corepressor 1; Histone H3.1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0, P68431
- Ligands
- FDA, CL
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 (EC 1.-.-.-) | protein | 664 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 63% helix, 0% strand | Q9UKL0 |
| E | Histone H3.1 | protein | 7 | 0% helix, 0% strand | P68431 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · chains A, E
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.87 | 0.95 | 78 | FDA |
| 2 | 359 | 0.63 | 0.79 | 28 | empty |
| 3 | 169 | 0.47 | 0.76 | 27 | empty |
| 4 | 95 | 0.44 | 0.79 | 19 | empty |
| 5 | 84 | 0.43 | 0.79 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2753 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 717 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2UXN · Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKL0 · AlphaFold monomer V2.0 prediction for rest corepressor 1 (Q9UKL0) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O60341
- Every structure of UniProt Q9UKL0
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 2UXN · PDBe 2UXN · UniProt O60341 · UniProt Q9UKL0 · UniProt P68431
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