MolNFT v1 · #140748 · protein
Crystal structure of arabidopsis thaliana JMJ14 catalytic domain in complex with nog and H3K4ME3 peptide
5YKO · Probable lysine-specific demethylase JMJ14: “Crystal structure of arabidopsis thaliana JMJ14 catalytic domain in complex with nog and H3K4ME3 peptide”. X-ray diffraction, 3 ligands (OGA, ZN, NI), 4 pockets (best druggability 0.69).…
- PDB
- 5YKO
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable lysine-specific demethylase JMJ14; H3(1-10)K4ME3 peptide
- EC
- 1.14.11.-
- UniProt
- Q8GUI6, P59226
- Ligands
- OGA, ZN, NI
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable lysine-specific demethylase JMJ14 (EC 1.14.11.-) | protein | 487 | 41% helix, 19% strand | Q8GUI6 |
| P | H3(1-10)K4ME3 peptide | protein | 7 | 0% helix, 14% strand | P59226 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, P
- ZN · Zinc ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A, P
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 | 164 | 0.69 | 0.88 | 28 | NI, OGA |
| 2 | 118 | 0.49 | 0.80 | 29 | empty |
| 3 | 90 | 0.46 | 0.80 | 15 | empty |
| 4 | 50 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–P · 664 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5YKO · Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and… · 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
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.54
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
- Every structure of UniProt P59226
- Elsewhere: RCSB PDB 5YKO · PDBe 5YKO · UniProt Q8GUI6 · UniProt P59226
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