Research workbench
Crystal structure of JMJD2A complexed with 5-carboxy-8- hydroxyquinoline
Analyse Crystal structure of JMJD2A complexed with 5-carboxy-8- hydroxyquinoline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NJY
- Type
- protein
- Length
- 694 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
- 8XQ, NI, ZN
- Pockets
- 9 · best druggability 0.72
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 | 347 | 32% helix, 24% strand | O75164 |
Ligands and binding sites
- 8XQ · 8-hydroxyquinoline-5-carboxylic 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.72 | 0.84 | 38 | NI, 8XQ |
| 2 | 372 | 0.72 | 0.83 | 45 | NI, 8XQ |
| 3 | 500 | 0.64 | 0.76 | 52 | empty |
| 4 | 107 | 0.49 | 0.80 | 24 | empty |
| 5 | 79 | 0.43 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NJY · Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline · 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 3NJY · PDBe 3NJY · UniProt O75164
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