Research workbench
A linked jumonji domain of the KDM5A lysine demethylase
Analyse A linked jumonji domain of the KDM5A lysine demethylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E6H
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- AKG, MN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 294 | 30% helix, 24% strand | P29375 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.67 | 0.81 | 37 | MN, AKG |
| 2 | 122 | 0.47 | 0.78 | 21 | GOL |
| 3 | 85 | 0.34 | 0.75 | 20 | empty |
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 P29375
- Elsewhere: RCSB PDB 5E6H · PDBe 5E6H · UniProt P29375
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