Research workbench
Swirm domain of human LSD1
Analyse Swirm domain of human LSD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IT3
- Type
- protein
- Length
- 170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A
- UniProt
- O60341
- Ligands
- MG
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific histone demethylase 1A | protein | 85 | 58% helix, 0% strand | O60341 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.49 | 0.78 | 22 | empty |
| 2 | 128 | 0.40 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 380 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5IT3 · Swirm domain of human Lsd1 · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 5IT3 · PDBe 5IT3 · UniProt O60341
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