MolNFT v1 · #125251 · protein
LSD1-COREST1 in complex with polymyxin E (colistin)
5L3G · Lysine-specific histone demethylase 1A: “LSD1-COREST1 in complex with polymyxin E (colistin)”. X-ray diffraction, 3 ligands (6F5, FAD, NA), 10 pockets (best druggability 0.87). MolNFT v1 #125251 on GenesisL1: 3D structure, binding…
- PDB
- 5L3G
- 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; Polymyxin E
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- 6F5, FAD, NA
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 45% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 68% helix, 0% strand | Q9UKL0 |
| C | Polymyxin E | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- 6F5 · 6-methylheptanoic acid · ligand · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
- NA · Sodium ion · metal · 2 copies · 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 | 404 | 0.87 | 0.95 | 72 | FAD |
| 2 | 186 | 0.71 | 0.88 | 31 | empty |
| 3 | 378 | 0.62 | 0.78 | 28 | empty |
| 4 | 188 | 0.49 | 0.76 | 27 | empty |
| 5 | 94 | 0.44 | 0.79 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2735 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 8 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 5L3G · PDBe 5L3G · UniProt O60341 · UniProt Q9UKL0
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