MolNFT v1 · #119500 · protein
Crystal structure of jmjc domain of human histone demethylase uty in complex with L-malate
5FY0: “Crystal structure of jmjc domain of human histone demethylase uty in complex with L-malate”. X-ray diffraction, 3 ligands (LMR, MN, ZN), 10 pockets (best druggability 0.74). MolNFT v1 #119500 on GenesisL1: 3D structure, binding…
- PDB
- 5FY0
- Type
- protein
- Length
- 883 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase uty
- UniProt
- O14607
- Ligands
- LMR, MN, ZN
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase uty | protein | 444 | 37% helix, 23% strand | O14607 |
| B | Histone demethylase uty | protein | 439 | 37% helix, 23% strand | O14607 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic 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 · 15 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.74 | 0.84 | 51 | EDO |
| 2 | 520 | 0.72 | 0.81 | 46 | MN, LMR, EDO |
| 3 | 481 | 0.70 | 0.80 | 45 | MN, LMR, EDO |
| 4 | 472 | 0.67 | 0.78 | 48 | empty |
| 5 | 246 | 0.60 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1110 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5FY0 · Crystal structure of JmjC domain of human histone demethylase UTY in complex with L-malate · 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 5FY0 · PDBe 5FY0 · UniProt O14607
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