Research workbench
JMJD2A complexed with R-2-hydroxyglutarate and histone H3K36ME3 peptide (30-41)
Analyse JMJD2A complexed with R-2-hydroxyglutarate and histone H3K36ME3 peptide (30-41) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YBP
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Histone H3.1T
- EC
- 1.14.11.-
- UniProt
- O75164, Q16695
- Ligands
- 2HG, NI, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 353 | 32% helix, 24% strand | O75164 |
| C, D | Histone H3.1T | protein | 12 | 0% helix, 8% strand | Q16695 |
Ligands and binding sites
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.78 | 0.97 | 26 | NI, 2HG |
| 2 | 110 | 0.78 | 0.97 | 26 | NI, 2HG |
| 3 | 100 | 0.49 | 0.81 | 28 | empty |
| 4 | 64 | 0.45 | 0.83 | 21 | empty |
| 5 | 205 | 0.45 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 979 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2YBP · JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) · the same entry in another collection · chain A against A, TM-score 1.00
- Q16695 · AlphaFold monomer V2.0 prediction for histone H3.1T (Q16695) · a predicted model of the same protein · chain C against A, TM-score 0.29
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
- Every structure of UniProt Q16695
- Elsewhere: RCSB PDB 2YBP · PDBe 2YBP · UniProt O75164 · UniProt Q16695
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