Research workbench
Crystal structure of arabidopsis thaliana JMJ14 catalytic domain in complex with nog and H3K4ME3 peptide
Analyse Crystal structure of arabidopsis thaliana JMJ14 catalytic domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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