MolNFT v1 · #54612 · protein
Crystal structure of JMJD3
2XUE · Lysine-specific demethylase 6B: “Crystal structure of JMJD3”. X-ray diffraction, 4 ligands (AKG, ZN, FE), 9 pockets (best druggability 0.71). MolNFT v1 #54612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XUE
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6B
- EC
- 1.14.11.-
- UniProt
- O15054
- Ligands
- AKG, ZN, FE, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 427 | 35% helix, 25% strand | O15054 |
| B | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 423 | 35% helix, 25% strand | O15054 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.71 | 0.81 | 48 | AKG |
| 2 | 477 | 0.67 | 0.79 | 50 | AKG |
| 3 | 227 | 0.57 | 0.79 | 29 | empty |
| 4 | 229 | 0.57 | 0.79 | 31 | empty |
| 5 | 318 | 0.55 | 0.75 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 O15054
- Elsewhere: RCSB PDB 2XUE · PDBe 2XUE · UniProt O15054
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