Research workbench
Crystal structure of LSD2-npac with H3 in space group P21
Analyse Crystal structure of LSD2-npac with H3 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
- 4GUR
- Type
- protein
- Length
- 766 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 H3.3
- EC
- 1.-.-.-
- UniProt
- Q8NB78, Q49A26, P84243
- Ligands
- FAD, ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 734 | 37% helix, 15% strand | Q8NB78 |
| B | Putative oxidoreductase GLYR1 (EC 1.-.-.-) | protein | 12 | 25% helix, 0% strand | Q49A26 |
| C | Histone H3.3 | protein | 20 | 15% helix, 0% strand | P84243 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.82 | 0.85 | 95 | FAD |
| 2 | 53 | 0.72 | 0.99 | 18 | empty |
| 3 | 112 | 0.63 | 0.88 | 32 | empty |
| 4 | 191 | 0.50 | 0.76 | 32 | empty |
| 5 | 55 | 0.36 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1305 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GUR · Crystal structure of LSD2-NPAC with H3 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 0.35
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain C against A, TM-score 0.20
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 P84243
- Elsewhere: RCSB PDB 4GUR · PDBe 4GUR · UniProt Q8NB78 · UniProt Q49A26 · UniProt P84243
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