Research workbench
Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase
Analyse Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q8E
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A; Histone 3 peptide
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- OGA, NI, ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 344 | 30% helix, 25% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 337 | 31% helix, 25% strand | O75164 |
| F | Histone 3 peptide | protein | 4 | 0% helix, 25% strand | — |
| G | Histone 3 peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, F, B, G
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.77 | 0.97 | 25 | OGA |
| 2 | 336 | 0.70 | 0.83 | 38 | NI, OGA |
| 3 | 567 | 0.65 | 0.76 | 47 | empty |
| 4 | 101 | 0.53 | 0.83 | 24 | empty |
| 5 | 114 | 0.53 | 0.82 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–G · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 500 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 397 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2Q8E · Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase · 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 2Q8E · PDBe 2Q8E · UniProt O75164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.