MolNFT v1 · #38169 · protein
Crystal structure of catalytic core domain of JMJD2A complexed with alpha-ketoglutarate
2GP5 · Jumonji domain-containing protein 2A: “Crystal structure of catalytic core domain of JMJD2A complexed with alpha-ketoglutarate”. X-ray diffraction, 3 ligands (AKG, ZN, FE2), 9 pockets (best druggability 0.71). MolNFT v1 #38169 on…
- PDB
- 2GP5
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jumonji domain-containing protein 2A
- UniProt
- O75164
- Ligands
- AKG, ZN, FE2
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jumonji domain-containing protein 2A | protein | 347 | 29% helix, 24% strand | O75164 |
| B | Jumonji domain-containing protein 2A | protein | 337 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE2 · Fe (II) 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.71 | 0.77 | 82 | empty |
| 2 | 380 | 0.71 | 0.83 | 37 | FE2, AKG |
| 3 | 431 | 0.71 | 0.82 | 40 | FE2, AKG |
| 4 | 76 | 0.45 | 0.81 | 20 | empty |
| 5 | 129 | 0.40 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GP5 · Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate · 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 2GP5 · PDBe 2GP5 · UniProt O75164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.