Research workbench
Native structure of LSD2/AOF1/KDM1B in spacegroup of I222 at 2.9A
Analyse Native structure of LSD2/AOF1/KDM1B in spacegroup of I222 at 2.9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FWJ
- Type
- protein
- Length
- 1,492 residues
- Chains
- 2
- 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, K, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% 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 |
| B | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 742 | 36% helix, 15% strand | Q8NB78 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.82 | 96 | FAD |
| 2 | 973 | 0.81 | 0.82 | 97 | FAD |
| 3 | 873 | 0.76 | 0.79 | 85 | empty |
| 4 | 559 | 0.71 | 0.79 | 49 | empty |
| 5 | 567 | 0.70 | 0.79 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1624 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4FWJ · Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A · 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 B 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 4FWJ · PDBe 4FWJ · UniProt Q8NB78
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