Research workbench
Crystal structure of jmjc domain of human histone demethylase uty in complex with succinate
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
- 5FY7
- Type
- protein
- Length
- 892 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase uty
- UniProt
- O14607
- Ligands
- MN, ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase uty | protein | 446 | 37% helix, 22% strand | O14607 |
| B | Histone demethylase uty | protein | 446 | 36% helix, 25% strand | O14607 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.79 | 0.81 | 88 | EDO |
| 2 | 521 | 0.71 | 0.80 | 45 | MN, SIN, EDO |
| 3 | 480 | 0.69 | 0.80 | 46 | MN, SIN, EDO |
| 4 | 273 | 0.62 | 0.79 | 25 | empty |
| 5 | 67 | 0.43 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5FY7 · 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 5FY7 · PDBe 5FY7 · UniProt O14607
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