Research workbench
The crystal structure of core JMJD2D complexed with fe and N- oxalylglycine
Analyse The crystal structure of core JMJD2D complexed with fe 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
- 3DXU
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3D
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- OGA, ZN, FE2, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3D (EC 1.14.11.-) | protein | 331 | 32% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- FE2 · Fe (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.73 | 0.82 | 56 | OGA, GOL |
| 2 | 107 | 0.47 | 0.79 | 27 | empty |
| 3 | 75 | 0.34 | 0.75 | 24 | GOL |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3DXU · The crystal structure of core JMJD2D complexed with FE 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 Q6B0I6
- Elsewhere: RCSB PDB 3DXU · PDBe 3DXU · UniProt Q6B0I6
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