MolNFT v1 · #154600 · protein
LSD1-corest-S2101 five-membered ring adduct model
6KGK · Lysine-specific histone demethylase 1A: “LSD1-corest-S2101 five-membered ring adduct model”. X-ray diffraction, 2 ligands (DJ0, FAD), 8 pockets (best druggability 0.82). MolNFT v1 #154600 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KGK
- Type
- protein
- Length
- 793 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- DJ0, FAD
- 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 1A (EC 1.-.-.-) | protein | 661 | 45% helix, 17% strand | O60341 |
| B | Rest corepressor 1 | protein | 132 | 64% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- DJ0 · 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · 3 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 | 871 | 0.82 | 0.84 | 97 | GOL, DJ0, FAD |
| 2 | 328 | 0.62 | 0.78 | 29 | empty |
| 3 | 148 | 0.44 | 0.75 | 26 | empty |
| 4 | 84 | 0.43 | 0.79 | 19 | empty |
| 5 | 144 | 0.40 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2718 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 Q9UKL0
- Elsewhere: RCSB PDB 6KGK · PDBe 6KGK · UniProt O60341 · UniProt Q9UKL0
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