Research workbench
Structure of JMJD2A complexed with inhibitor 10A
Analyse Structure of JMJD2A complexed with inhibitor 10A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWJ
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.27
- UniProt
- O75164
- Ligands
- Y28, NI, ZN
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.27) | protein | 346 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.27) | protein | 347 | 28% helix, 24% strand | O75164 |
Ligands and binding sites
- Y28 · O-benzyl-N-(carboxycarbonyl)-D-tyrosine · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.72 | 0.84 | 36 | NI, Y28 |
| 2 | 386 | 0.70 | 0.82 | 36 | NI, Y28 |
| 3 | 577 | 0.68 | 0.77 | 71 | empty |
| 4 | 126 | 0.50 | 0.80 | 25 | empty |
| 5 | 209 | 0.47 | 0.74 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 472 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 O75164
- Elsewhere: RCSB PDB 2WWJ · PDBe 2WWJ · UniProt O75164
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