MolNFT v1 · #97958 · protein
Structure of LSD1-corest-tetrahydrofolate complex
4KUM · Lysine-specific histone demethylase 1A: “Structure of LSD1-corest-tetrahydrofolate complex”. X-ray diffraction, 3 ligands (FAD, THG, CL), 11 pockets (best druggability 0.82). MolNFT v1 #97958 on GenesisL1: 3D structure, binding…
- PDB
- 4KUM
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1
- UniProt
- O60341, J3KN32
- Ligands
- FAD, THG, CL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A | protein | 666 | 45% helix, 17% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 64% helix, 0% strand | J3KN32 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- THG · (6S)-5,6,7,8-tetrahydrofolate · ligand · chains A
- CL · Chloride ion · ion · 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 | 1031 | 0.82 | 0.83 | 89 | FAD, THG |
| 2 | 380 | 0.64 | 0.78 | 29 | empty |
| 3 | 168 | 0.47 | 0.76 | 25 | empty |
| 4 | 82 | 0.45 | 0.80 | 18 | empty |
| 5 | 111 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2750 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 J3KN32
- Elsewhere: RCSB PDB 4KUM · PDBe 4KUM · UniProt O60341 · UniProt J3KN32
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