MolNFT v1 · #40553 · protein
Structural basis for corest-dependent demethylation of nucleosomes by the human LSD1 histone demethylase
2IW5 · Lysine-specific histone demethylase 1: “Structural basis for corest-dependent demethylation of nucleosomes by the human LSD1 histone demethylase”. X-ray diffraction, 3 ligands (FAD, CL, NH4), 8 pockets (best druggability 0.82).…
- PDB
- 2IW5
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1; Rest corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD, CL, NH4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 (EC 1.-.-.-) | protein | 666 | 45% helix, 17% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 63% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- NH4 · Ammonium ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.82 | 0.83 | 91 | FAD, GOL, NH4 |
| 2 | 360 | 0.63 | 0.79 | 28 | empty |
| 3 | 188 | 0.48 | 0.76 | 28 | empty |
| 4 | 97 | 0.44 | 0.79 | 16 | empty |
| 5 | 108 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2799 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2IW5 · Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1… · 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
- Elsewhere: RCSB PDB 2IW5 · PDBe 2IW5 · UniProt O60341 · UniProt Q9UKL0
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