MolNFT v1 · #125250 · protein
LSD1-COREST1 in complex with polymyxin B
5L3F · Lysine-specific histone demethylase 1A: “LSD1-COREST1 in complex with polymyxin B”. X-ray diffraction, 2 ligands (6FH, FAD), 10 pockets (best druggability 0.86). MolNFT v1 #125250 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L3F
- 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; Polmyxin B
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- 6FH, FAD
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 45% helix, 15% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 65% helix, 0% strand | Q9UKL0 |
| C | Polmyxin B | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- 6FH · (6~{S})-6-methyloctanoic acid · ligand · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.86 | 0.94 | 72 | FAD |
| 2 | 188 | 0.67 | 0.85 | 33 | empty |
| 3 | 395 | 0.63 | 0.78 | 33 | empty |
| 4 | 204 | 0.49 | 0.76 | 23 | empty |
| 5 | 113 | 0.46 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2686 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 768 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 d-amino, 1 covalent (nonstandard, D-amino acid, covalent ligand).
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 5L3F · PDBe 5L3F · UniProt O60341 · UniProt Q9UKL0
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