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Crystal structure of lysine specific demethylase 1 (LSD1) with tak- 418, FAD-adduct
Analyse Crystal structure of lysine specific demethylase 1 (LSD1) with tak- 418… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E0G
- Type
- protein
- Length
- 641 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A
- EC
- 1.14.99.66
- UniProt
- O60341
- Ligands
- HUF, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.14.99.66) | protein | 641 | 45% helix, 17% strand | O60341 |
Ligands and binding sites
- HUF · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- IMD · Imidazole · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.82 | 0.83 | 89 | HUF, IMD |
| 2 | 363 | 0.61 | 0.77 | 36 | empty |
| 3 | 54 | 0.49 | 0.86 | 17 | empty |
| 4 | 197 | 0.48 | 0.76 | 23 | empty |
| 5 | 94 | 0.41 | 0.77 | 17 | empty |
Compared structures
- 7E0G · Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 7E0G · PDBe 7E0G · UniProt O60341
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