Research workbench
Structure of LSD1:COREST in complex with ssrna
Analyse Structure of LSD1:COREST in complex with ssrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XBF
- Type
- protein + RNA
- 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; RNA (5'-R(*UP*UP*AP*GP*G)-3')
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD, SO4
- Pockets
- 9 · best druggability 0.82
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 | 63% helix, 0% strand | Q9UKL0 |
| D | RNA (5'-R(*UP*UP*AP*GP*G)-3') | rna | 4 | — | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.82 | 0.83 | 89 | FAD |
| 2 | 380 | 0.64 | 0.78 | 34 | empty |
| 3 | 215 | 0.51 | 0.76 | 25 | empty |
| 4 | 93 | 0.46 | 0.80 | 19 | empty |
| 5 | 89 | 0.39 | 0.77 | 20 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 2756 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 237 Ų buried · 7 hydrogen bonds · protein-nucleic
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 4XBF · PDBe 4XBF · UniProt O60341 · UniProt Q9UKL0
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