MolNFT v1 · #163441 · protein
LSD1/COREST1 complex with macrocyclic peptide inhibitor
6S35 · Lysine-specific histone demethylase 1A: “LSD1/COREST1 complex with macrocyclic peptide inhibitor”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.87). MolNFT v1 #163441 on GenesisL1: 3D structure, binding sites…
- PDB
- 6S35
- Type
- protein
- Length
- 803 residues
- Chains
- 3
- 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
- FAD
- Pockets
- 8 · best druggability 0.87
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 | 45% helix, 15% strand | O60341 |
| B | Rest corepressor 1 | protein | 134 | 61% helix, 0% strand | Q9UKL0 |
| C | Ala-arg-(D)LYS-met-gln-glu-ala-arg-lys-ser-thr | protein | 7 | 0% helix, 0% strand | — |
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
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 | 755 | 0.87 | 0.90 | 90 | FAD |
| 2 | 321 | 0.61 | 0.78 | 27 | empty |
| 3 | 174 | 0.48 | 0.77 | 24 | empty |
| 4 | 87 | 0.44 | 0.79 | 19 | empty |
| 5 | 103 | 0.41 | 0.76 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2854 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 d-amino, 1 isopeptide (D-amino acid, isopeptide).
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 6S35 · PDBe 6S35 · UniProt O60341 · UniProt Q9UKL0
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