Research workbench
Crystal structure of jmjc domain of human histone demethylase uty
Analyse Crystal structure of jmjc domain of human histone demethylase uty in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZLI
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase uty
- EC
- 1.14.11.-
- UniProt
- O14607
- Ligands
- AKG, FE2, ZN
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase uty (EC 1.14.11.-) | protein | 442 | 37% helix, 24% strand | O14607 |
| B | Histone demethylase uty (EC 1.14.11.-) | protein | 438 | 37% helix, 24% strand | O14607 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.80 | 0.81 | 104 | empty |
| 2 | 567 | 0.73 | 0.81 | 55 | EDO, AKG, FE2 |
| 3 | 477 | 0.70 | 0.81 | 44 | EDO, AKG, FE2 |
| 4 | 260 | 0.60 | 0.79 | 25 | empty |
| 5 | 99 | 0.42 | 0.77 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3ZLI · Crystal structure of JmjC domain of human histone demethylase UTY · the same entry in another collection · chain A against A, TM-score 1.00
- O14607 · AlphaFold monomer V2.0 prediction for histone demethylase uty (O14607) · a predicted model of the same protein · chain B 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 O14607
- Elsewhere: RCSB PDB 3ZLI · PDBe 3ZLI · UniProt O14607
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