MolNFT v1 · #93180 · protein
Crystal structure of LSD2-npac
4GUT · Lysine-specific histone demethylase 1B: “Crystal structure of LSD2-npac”. X-ray diffraction, 2 ligands (FAD, ZN), 10 pockets (best druggability 0.80). MolNFT v1 #93180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GUT
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1B; Putative oxidoreductase GLYR1
- EC
- 1.-.-.-
- UniProt
- Q8NB78, Q49A26
- Ligands
- FAD, ZN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 740 | 37% helix, 15% strand | Q8NB78 |
| B | Putative oxidoreductase GLYR1 (EC 1.-.-.-) | protein | 12 | 25% helix, 0% strand | Q49A26 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.80 | 0.82 | 101 | FAD, GOL |
| 2 | 53 | 0.73 | 0.99 | 18 | empty |
| 3 | 131 | 0.65 | 0.87 | 33 | empty |
| 4 | 78 | 0.46 | 0.82 | 16 | empty |
| 5 | 110 | 0.39 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4GUT · Crystal structure of LSD2-NPAC · 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 0.99
- Q49A26 · AlphaFold monomer V2.0 prediction for putative oxidoreductase GLYR1 (Q49A26) · a predicted model of the same protein · chain B against A, TM-score 0.37
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
- Elsewhere: RCSB PDB 4GUT · PDBe 4GUT · UniProt Q8NB78 · UniProt Q49A26
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