MolNFT v1 · #47258 · protein
Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at LYS9
2OT7 · Jmjc domain-containing histone demethylation protein 3A: “Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at LYS9”. X-ray diffraction, 3 ligands (OGA, NI, ZN), 9 pockets (best druggability 0.78). MolNFT…
- 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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