Research workbench
Crystal structure of LSD1-corest in complex with a N- terminal snail peptide
Analyse Crystal structure of LSD1-corest in complex with a N- terminal snail peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y48
- Type
- protein
- Length
- 807 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 1A; Rest corepressor 1; Zinc finger protein SNAI1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0, O95863
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 1A (EC 1.-.-.-) | protein | 665 | 45% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
| C | Zinc finger protein SNAI1 | protein | 9 | 33% helix, 0% strand | O95863 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.85 | 0.92 | 78 | FAD |
| 2 | 355 | 0.62 | 0.78 | 30 | empty |
| 3 | 226 | 0.49 | 0.75 | 22 | empty |
| 4 | 99 | 0.47 | 0.80 | 19 | empty |
| 5 | 93 | 0.40 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2792 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2Y48 · Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL 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
- O95863 · AlphaFold monomer V2.0 prediction for zinc finger protein SNAI1 (O95863) · a predicted model of the same protein · chain C against A, TM-score 0.41
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
- Every structure of UniProt O95863
- Elsewhere: RCSB PDB 2Y48 · PDBe 2Y48 · UniProt O60341 · UniProt Q9UKL0 · UniProt O95863
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