Research workbench
Crystal structure of human JMJD2A in complex with fumarate
Analyse Crystal structure of human JMJD2A in complex with fumarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYH
- 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
- FUM, ZN, MN, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 351 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 31% helix, 25% strand | O75164 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
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 | 428 | 0.73 | 0.83 | 39 | FUM, MN |
| 2 | 417 | 0.70 | 0.81 | 38 | FUM, MN |
| 3 | 581 | 0.66 | 0.76 | 68 | empty |
| 4 | 111 | 0.49 | 0.80 | 24 | empty |
| 5 | 238 | 0.49 | 0.74 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FYH · Crystal structure of human JMJD2A in complex with fumarate · 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 5FYH · PDBe 5FYH · UniProt O75164
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