Research workbench
Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at LYS9
Analyse Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OT7
- 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; Histone 3 K9 monomethyl
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- OGA, 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 | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 349 | 31% helix, 24% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 348 | 30% helix, 25% strand | O75164 |
| C, D | Histone 3 K9 monomethyl | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.78 | 0.99 | 19 | NI, OGA |
| 2 | 86 | 0.77 | 0.99 | 19 | NI, OGA |
| 3 | 584 | 0.68 | 0.77 | 68 | empty |
| 4 | 164 | 0.54 | 0.80 | 27 | empty |
| 5 | 166 | 0.54 | 0.80 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 764 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation, methylation).
Compared structures
- 2OT7 · Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated 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 2OT7 · PDBe 2OT7 · UniProt O75164
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