MolNFT v1 · #53635 · protein
Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1.
2X0L · Lysine-specific histone demethylase 1: “Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1.”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.85). MolNFT v1 #53635 on…
- PDB
- 2X0L
- Type
- protein
- Length
- 819 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 peptide
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0, Q5TEC6
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 (EC 1.-.-.-) | protein | 670 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
| C | Histone H3 peptide | protein | 16 | 19% helix, 0% strand | Q5TEC6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.85 | 0.94 | 56 | FAD |
| 2 | 390 | 0.62 | 0.78 | 36 | empty |
| 3 | 229 | 0.53 | 0.77 | 23 | empty |
| 4 | 92 | 0.45 | 0.79 | 19 | empty |
| 5 | 86 | 0.39 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2769 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1138 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2X0L · Crystal structure of a neuro-specific splicing variant of human histone lysine… · 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
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain C against A, TM-score 0.18
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 Q5TEC6
- Elsewhere: RCSB PDB 2X0L · PDBe 2X0L · UniProt O60341 · UniProt Q9UKL0 · UniProt Q5TEC6
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