MolNFT v1 · #119504 · protein
Crystal structure of jmjc domain of human histone demethylase uty in complex with succinate
5FY7: “Crystal structure of jmjc domain of human histone demethylase uty in complex with succinate”. X-ray diffraction, 2 ligands (MN, ZN), 10 pockets (best druggability 0.79). MolNFT v1 #119504 on GenesisL1: 3D structure, binding sites…
- 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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