Research workbench
The crystal structure of JMJD2A complexed with ni and N-oxalylglycine
Analyse The crystal structure of JMJD2A complexed with ni and N-oxalylglycine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OQ7
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A
- EC
- 1.14.11.27
- UniProt
- O75164
- Ligands
- OGA, NI, ZN
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.27) | protein | 346 | 30% helix, 25% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.27) | protein | 347 | 29% helix, 24% strand | O75164 |
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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.72 | 0.84 | 42 | NI, OGA |
| 2 | 365 | 0.69 | 0.82 | 38 | OGA |
| 3 | 508 | 0.62 | 0.75 | 44 | empty |
| 4 | 118 | 0.50 | 0.80 | 26 | empty |
| 5 | 103 | 0.50 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 343 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2OQ7 · The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine · 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 2OQ7 · PDBe 2OQ7 · UniProt O75164
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