MolNFT v1 · #55155 · protein
JMJD2A complexed with R-2-hydroxyglutarate
2YBK · Lysine-specific demethylase 4A: “JMJD2A complexed with R-2-hydroxyglutarate”. X-ray diffraction, 4 ligands (2HG, NI, ZN), 7 pockets (best druggability 0.71). MolNFT v1 #55155 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2YBK
- Type
- protein
- Length
- 698 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
- 2HG, NI, ZN, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 32% helix, 24% strand | O75164 |
Ligands and binding sites
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · 2 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 · 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 | 406 | 0.71 | 0.82 | 43 | NI, 2HG |
| 2 | 652 | 0.70 | 0.78 | 73 | empty |
| 3 | 405 | 0.70 | 0.82 | 42 | NI, 2HG |
| 4 | 107 | 0.49 | 0.81 | 22 | empty |
| 5 | 161 | 0.41 | 0.73 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 360 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YBK · JMJD2A complexed with R-2-hydroxyglutarate · 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 2YBK · PDBe 2YBK · UniProt O75164
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