MolNFT v1 · #85623 · protein
JMJD2A complexed with daminozide
4AI9 · Lysine-specific demethylase 4A: “JMJD2A complexed with daminozide”. X-ray diffraction, 4 ligands (DZA, NI, ZN), 9 pockets (best druggability 0.72). MolNFT v1 #85623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AI9
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- DZA, NI, ZN, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- DZA · Daminozide · ligand · 3 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.72 | 0.83 | 43 | NI, DZA |
| 2 | 434 | 0.71 | 0.82 | 41 | NI, DZA |
| 3 | 647 | 0.67 | 0.76 | 75 | empty |
| 4 | 129 | 0.54 | 0.82 | 24 | empty |
| 5 | 228 | 0.47 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 377 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4AI9 · JMJD2A Complexed with Daminozide · the same entry in another collection · 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 O75164
- Elsewhere: RCSB PDB 4AI9 · PDBe 4AI9 · UniProt O75164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.