Research workbench
Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at LYS9
Analyse Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OX0
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A; Synthetic peptide
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- OGA, NI, ZN, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 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 | 349 | 31% helix, 25% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 348 | 30% helix, 25% strand | O75164 |
| C, D | Synthetic peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.79 | 0.99 | 20 | NI, OGA |
| 2 | 81 | 0.77 | 0.99 | 20 | NI, OGA |
| 3 | 291 | 0.64 | 0.81 | 56 | empty |
| 4 | 491 | 0.62 | 0.75 | 47 | empty |
| 5 | 186 | 0.53 | 0.78 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 788 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 788 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation, methylation).
Compared structures
- 2OX0 · Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9 · 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 2OX0 · PDBe 2OX0 · UniProt O75164
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