Research workbench
LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1R,2S)
Analyse LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1R,2S) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UVA
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- HOMO SAPIENS
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- D73
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- D73 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aS)-4a-[(1S,3E)-3-imino-1-phenylbutyl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.83 | 0.83 | 91 | D73 |
| 2 | 314 | 0.61 | 0.78 | 29 | empty |
| 3 | 195 | 0.47 | 0.75 | 24 | empty |
| 4 | 89 | 0.44 | 0.79 | 19 | empty |
| 5 | 122 | 0.41 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2787 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4UVA · LSD1(KDM1A)-corest in complex with 1-methyl-tranylcypromine (1R,2S) · the same entry in another collection · chain A against A, TM-score 1.00
- O60341 · AlphaFold monomer V2.0 prediction for lysine-specific histone demethylase 1A (O60341) · a predicted model of the same protein · 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 4UVA · PDBe 4UVA · UniProt O60341 · UniProt Q9UKL0
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