Research workbench
LSD1-CoREST-S2101 N5 adduct model
Analyse LSD1-CoREST-S2101 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
- 6KGL
- Type
- protein
- Length
- 793 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Lysine-specific histone demethylase 1A; REST corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- DJ0, FAD
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.7 · 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.82 | 0.84 | 98 | GOL, DJ0, FAD |
| 2 | 335 | 0.62 | 0.78 | 29 | empty |
| 3 | 149 | 0.43 | 0.75 | 26 | empty |
| 4 | 80 | 0.43 | 0.79 | 19 | empty |
| 5 | 147 | 0.40 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2712 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6KGL · LSD1-corest-S2101 N5 adduct model · 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 6KGL · PDBe 6KGL · UniProt O60341 · UniProt Q9UKL0
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