Research workbench
Crystal structure of the swirm domain of human histone lysine-specific demethylase LSD1
Analyse Crystal structure of the swirm domain of human histone lysine-specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E1F
- Type
- protein
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A
- EC
- 1.-.-.-
- UniProt
- O60341
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 89 | 58% helix, 0% strand | O60341 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.78 | 0.80 | 90 | empty |
| 2 | 312 | 0.63 | 0.80 | 44 | empty |
| 3 | 129 | 0.43 | 0.76 | 16 | empty |
| 4 | 120 | 0.40 | 0.75 | 16 | empty |
| 5 | 89 | 0.34 | 0.74 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 119 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 116 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E1F · Crystal structure of the SWIRM domain of human histone lysine-specific demethylase 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 6E1F · PDBe 6E1F · UniProt O60341
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