Research workbench
Crystal structure of jmjc domain of human histone demethylase uty in complex with D-2-hydroxyglutarate
Analyse Crystal structure of jmjc domain of human histone demethylase uty in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYM
- Type
- protein
- Length
- 890 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
- 2HG, MN, ZN
- Pockets
- 9 · 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 | 444 | 37% helix, 23% strand | O14607 |
| B | Histone demethylase uty (EC 1.14.11.-) | protein | 446 | 36% helix, 25% strand | O14607 |
Ligands and binding sites
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 28 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.80 | 0.81 | 100 | EDO |
| 2 | 485 | 0.70 | 0.80 | 44 | MN, 2HG, EDO |
| 3 | 441 | 0.68 | 0.80 | 41 | MN, 2HG, EDO |
| 4 | 251 | 0.60 | 0.79 | 24 | EDO |
| 5 | 160 | 0.46 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1157 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5FYM · Crystal structure of JmjC domain of human histone demethylase UTY in complex with… · 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 A against A, TM-score 0.98
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 5FYM · PDBe 5FYM · UniProt O14607
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