MolNFT v1 · #92078 · protein
Complex structure of LSD2/AOF1/KDM1B with H3K4 mimic
4FWF · Lysine-specific histone demethylase 1B: “Complex structure of LSD2/AOF1/KDM1B with H3K4 mimic”. X-ray diffraction, 2 ligands (FAD, ZN), 9 pockets (best druggability 0.83). MolNFT v1 #92078 on GenesisL1: 3D structure, binding sites…
- PDB
- 4FWF
- 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; Histone H3.1
- EC
- 1.-.-.-
- UniProt
- Q8NB78, P68431
- Ligands
- FAD, ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 739 | 36% helix, 15% strand | Q8NB78 |
| E | Histone H3.1 | protein | 13 | 23% helix, 0% strand | P68431 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.83 | 0.90 | 84 | FAD |
| 2 | 505 | 0.71 | 0.81 | 45 | empty |
| 3 | 97 | 0.69 | 0.92 | 25 | empty |
| 4 | 113 | 0.44 | 0.78 | 18 | empty |
| 5 | 87 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–E · 933 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4FWF · Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic · 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
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 P68431
- Elsewhere: RCSB PDB 4FWF · PDBe 4FWF · UniProt Q8NB78 · UniProt P68431
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