Research workbench
LSD1-corest-S2116 N5 adduct model
Analyse LSD1-corest-S2116 N5 adduct model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KGN
- 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
- 7 · 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 · 5 copies · 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 | 959 | 0.82 | 0.84 | 94 | GOL, DJ0, FAD |
| 2 | 336 | 0.61 | 0.78 | 30 | GOL |
| 3 | 146 | 0.44 | 0.76 | 29 | empty |
| 4 | 80 | 0.41 | 0.78 | 18 | empty |
| 5 | 97 | 0.39 | 0.76 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 2722 Ų buried · 21 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 6KGN · PDBe 6KGN · UniProt O60341 · UniProt Q9UKL0
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