MolNFT v1 · #149907 · protein
Crystal structure of 2OG oxygenase JMJD6 (aa 1-343) in complex with FE(II) and 2OG
6GDY · Bifunctional arginine demethylase and lysyl-hydroxylase…: “Crystal structure of 2OG oxygenase JMJD6 (aa 1-343) in complex with FE(II) and 2OG”. X-ray diffraction, 4 ligands (AKG, FE, NA), 5 pockets (best druggability 0.81). MolNFT…
- PDB
- 6GDY
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
- EC
- 1.14.11.-
- UniProt
- Q6NYC1
- Ligands
- AKG, FE, NA, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 333 | 42% helix, 21% strand | Q6NYC1 |
| B | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 334 | 43% helix, 21% strand | Q6NYC1 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.81 | 0.83 | 115 | GOL, PO4 |
| 2 | 382 | 0.65 | 0.79 | 41 | FE, AKG, GOL |
| 3 | 389 | 0.64 | 0.78 | 34 | FE, AKG |
| 4 | 58 | 0.27 | 0.73 | 15 | empty |
| 5 | 50 | 0.23 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GDY · Crystal structure of 2OG oxygenase JMJD6 (aa 1-343) in complex with Fe(II) and 2OG · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NYC1 · AlphaFold monomer V2.0 prediction for bifunctional arginine demethylase and… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6NYC1
- Elsewhere: RCSB PDB 6GDY · PDBe 6GDY · UniProt Q6NYC1
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