Research workbench
Crystal structure of a truncated LSD1:COREST in the presence of an LSD1-nt peptide
Analyse Crystal structure of a truncated LSD1:COREST in the presence of an LSD1-nt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WC6
- Type
- protein
- Length
- 814 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1; LSD1-nt peptide
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 46% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 63% helix, 0% strand | Q9UKL0 |
| C | LSD1-nt peptide | protein | 15 | 87% helix, 0% strand | O60341 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.83 | 0.84 | 91 | FAD |
| 2 | 364 | 0.63 | 0.78 | 30 | empty |
| 3 | 348 | 0.61 | 0.77 | 29 | empty |
| 4 | 201 | 0.50 | 0.76 | 26 | empty |
| 5 | 99 | 0.47 | 0.80 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2786 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 6WC6 · Crystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide · the same entry in another collection · 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 0.96
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 6WC6 · PDBe 6WC6 · UniProt O60341 · UniProt Q9UKL0
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