Research workbench
Crystal structure of human JMJD2A in complex with compound 44
Analyse Crystal structure of human JMJD2A in complex with compound 44 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A7S
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- HOMO SAPIENS
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.27, 1.14.11.-
- UniProt
- O75164
- Ligands
- S2X, MN, ZN
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 345 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 351 | 29% helix, 24% strand | O75164 |
Ligands and binding sites
- S2X · 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.72 | 0.83 | 41 | MN, EDO, S2X |
| 2 | 403 | 0.72 | 0.83 | 39 | MN, EDO, S2X |
| 3 | 474 | 0.63 | 0.76 | 48 | empty |
| 4 | 212 | 0.56 | 0.79 | 37 | EDO |
| 5 | 106 | 0.55 | 0.84 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 431 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5A7S · Crystal structure of human JMJD2A in complex with compound 44 · the same entry in another collection · chain A against A, TM-score 1.00
- O75164 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4A (O75164) · a predicted model of the same protein · 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 5A7S · PDBe 5A7S · UniProt O75164
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