MolNFT v1 · #92077 · protein
Native structure of LSD2 /AOF1/KDM1B in spacegroup of C2221 at 2.13A
4FWE · Lysine-specific histone demethylase 1B: “Native structure of LSD2 /AOF1/KDM1B in spacegroup of C2221 at 2.13A”. X-ray diffraction, 2 ligands (FAD, ZN), 7 pockets (best druggability 0.81). MolNFT v1 #92077 on GenesisL1: 3D structure…
- PDB
- 4FWE
- Type
- protein
- Length
- 750 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1B
- EC
- 1.-.-.-
- UniProt
- Q8NB78
- Ligands
- FAD, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 750 | 37% helix, 15% strand | Q8NB78 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.81 | 0.83 | 96 | FAD |
| 2 | 492 | 0.68 | 0.78 | 45 | empty |
| 3 | 99 | 0.64 | 0.89 | 26 | empty |
| 4 | 106 | 0.41 | 0.77 | 28 | empty |
| 5 | 57 | 0.31 | 0.75 | 18 | empty |
Compared structures
- 4FWE · Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A · 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
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
- Elsewhere: RCSB PDB 4FWE · PDBe 4FWE · UniProt Q8NB78
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