Research workbench
Crystal structure of the catalytic core domain of JMJD2A
Analyse Crystal structure of the catalytic core domain of JMJD2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GP3
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jumonji domain-containing protein 2A
- UniProt
- O75164
- Ligands
- ZN, FE2
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jumonji domain-containing protein 2A | protein | 349 | 30% helix, 24% strand | O75164 |
| B | Jumonji domain-containing protein 2A | protein | 339 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.72 | 0.83 | 37 | FE2 |
| 2 | 408 | 0.71 | 0.82 | 41 | FE2 |
| 3 | 724 | 0.71 | 0.78 | 60 | empty |
| 4 | 75 | 0.48 | 0.83 | 20 | empty |
| 5 | 171 | 0.47 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2GP3 · Crystal structure of the catalytic core domain of jmjd2a · 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 2GP3 · PDBe 2GP3 · UniProt O75164
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