Research workbench
JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide
Analyse JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQS
- Type
- protein
- Length
- 229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A; Methylated histone H4 peptide
- EC
- 1.14.11.-
- UniProt
- O75164
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 109 | 6% helix, 50% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 108 | 9% helix, 51% strand | O75164 |
| C | Methylated histone H4 peptide | protein | 5 | 0% helix, 0% strand | — |
| D | Methylated histone H4 peptide | protein | 7 | 0% helix, 14% strand | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.52 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–D · 557 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 192 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 163 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2QQS · JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide · 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 2QQS · PDBe 2QQS · UniProt O75164
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