Research workbench
Crystal structure of LSD2-npac with H3(1-26)IN space group P21
Analyse Crystal structure of LSD2-npac with H3(1-26)IN space group P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HSU
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1B; Putative oxidoreductase GLYR1; Histone H3
- EC
- 1.-.-.-
- UniProt
- Q8NB78, Q49A26, Q92133
- Ligands
- FAD, ZN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 737 | 36% helix, 16% strand | Q8NB78 |
| B | Putative oxidoreductase GLYR1 (EC 1.-.-.-) | protein | 12 | 25% helix, 0% strand | Q49A26 |
| C | Histone H3 | protein | 26 | 12% helix, 8% strand | Q92133 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.85 | 0.95 | 62 | FAD |
| 2 | 50 | 0.71 | 0.99 | 19 | empty |
| 3 | 402 | 0.64 | 0.78 | 51 | empty |
| 4 | 176 | 0.63 | 0.84 | 42 | empty |
| 5 | 120 | 0.43 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1640 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 884 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HSU · Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NB78 · AlphaFold monomer V2.0 prediction for lysine-specific histone demethylase 1B (Q8NB78) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q49A26 · AlphaFold monomer V2.0 prediction for putative oxidoreductase GLYR1 (Q49A26) · a predicted model of the same protein · chain B against A, TM-score 0.46
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 Q8NB78
- Every structure of UniProt Q49A26
- Every structure of UniProt Q92133
- Elsewhere: RCSB PDB 4HSU · PDBe 4HSU · UniProt Q8NB78 · UniProt Q49A26 · UniProt Q92133
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