Research workbench
Crystal structure of LSD1-corest in complex with (-)-trans- 2-phenylcyclopropyl-1-amine
Analyse Crystal structure of LSD1-corest in complex with (-)-trans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XAJ
- 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, TCA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 (EC 1.-.-.-) | protein | 666 | 45% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 63% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- TCA · Phenylethylenecarboxylic acid · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.83 | 0.84 | 93 | FAD, TCA |
| 2 | 373 | 0.63 | 0.78 | 37 | empty |
| 3 | 254 | 0.53 | 0.76 | 29 | empty |
| 4 | 95 | 0.48 | 0.81 | 19 | empty |
| 5 | 79 | 0.41 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2761 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2XAJ · Crystal structure of LSD1-CoREST in complex with (-)-trans-2- phenylcyclopropyl-1-amine · 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 0.95
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 2XAJ · PDBe 2XAJ · UniProt O60341 · UniProt Q9UKL0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.