Research workbench
Crystal structure of JOX2 in complex with 2OG, fe, and ja
Analyse Crystal structure of JOX2 in complex with 2OG, fe, and ja in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LSV
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 2-oxoglutarate-dependent dioxygenase AT5G05600
- EC
- 1.14.11.-
- UniProt
- Q9FFF6
- Ligands
- AKG, JAA, FE
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 2-oxoglutarate-dependent dioxygenase AT5G05600 (EC 1.14.11.-) | protein | 338 | 30% helix, 20% strand | Q9FFF6 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- JAA · {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.83 | 0.87 | 75 | empty |
| 2 | 189 | 0.82 | 0.96 | 32 | AKG, JAA, FE |
| 3 | 188 | 0.82 | 0.96 | 33 | AKG, JAA, FE |
| 4 | 424 | 0.60 | 0.76 | 51 | empty |
| 5 | 338 | 0.58 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LSV · Crystal structure of JOX2 in complex with 2OG, Fe, and JA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FFF6 · AlphaFold monomer V2.0 prediction for probable 2-oxoglutarate- dependent dioxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9FFF6
- Elsewhere: RCSB PDB 6LSV · PDBe 6LSV · UniProt Q9FFF6
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