Research workbench
Crystal structure of arabidopsis thaliana JMJ14 catalytic domain
Analyse Crystal structure of arabidopsis thaliana JMJ14 catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKN
- Type
- protein
- Length
- 478 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable lysine-specific demethylase JMJ14
- EC
- 1.14.11.-
- UniProt
- Q8GUI6
- Ligands
- ZN, NI
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable lysine-specific demethylase JMJ14 (EC 1.14.11.-) | protein | 478 | 39% helix, 19% strand | Q8GUI6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.68 | 0.82 | 40 | NI |
| 2 | 92 | 0.45 | 0.80 | 16 | empty |
| 3 | 91 | 0.41 | 0.78 | 17 | empty |
| 4 | 51 | 0.30 | 0.76 | 15 | empty |
Compared structures
- 5YKN · crystal structure of Arabidopsis thaliana JMJ14 catalytic domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GUI6 · AlphaFold monomer V2.0 prediction for probable lysine-specific demethylase JMJ14 (Q8GUI6) · 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 Q8GUI6
- Elsewhere: RCSB PDB 5YKN · PDBe 5YKN · UniProt Q8GUI6
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