MolNFT v1 · #139135 · protein
Crystal structure of LSD1-corest in complex with peptide 9
5X60 · Lysine-specific histone demethylase 1A: “Crystal structure of LSD1-corest in complex with peptide 9”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.85). MolNFT v1 #139135 on GenesisL1: 3D structure, binding sites…
- PDB
- 5X60
- Type
- protein
- Length
- 809 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1; Peptide srtmqtarkstggkaprkql
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 662 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 132 | 63% helix, 0% strand | Q9UKL0 |
| C | Peptide srtmqtarkstggkaprkql | protein | 15 | 20% helix, 0% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
- 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 | 316 | 0.85 | 0.95 | 52 | FAD |
| 2 | 299 | 0.61 | 0.79 | 27 | GOL |
| 3 | 68 | 0.42 | 0.81 | 13 | empty |
| 4 | 74 | 0.41 | 0.79 | 16 | empty |
| 5 | 81 | 0.39 | 0.78 | 22 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 2703 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1109 Ų buried · 23 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 5X60 · PDBe 5X60 · UniProt O60341 · UniProt Q9UKL0
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