MolNFT v1 · #119496 · protein
Crystal structure of jmjc domain of human histone demethylase uty in complex with fumarate
5FXW: “Crystal structure of jmjc domain of human histone demethylase uty in complex with fumarate”. X-ray diffraction, 3 ligands (FUM, ZN, MN), 9 pockets (best druggability 0.80). MolNFT v1 #119496 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FXW
- 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
- FUM, ZN, MN
- Pockets
- 9 · best druggability 0.80
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 | 36% helix, 23% strand | O14607 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) 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
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 | 968 | 0.80 | 0.81 | 108 | EDO |
| 2 | 493 | 0.71 | 0.81 | 44 | MN, FUM, EDO |
| 3 | 461 | 0.69 | 0.80 | 45 | MN, FUM, EDO |
| 4 | 252 | 0.60 | 0.79 | 24 | empty |
| 5 | 99 | 0.46 | 0.80 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1146 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5FXW · Crystal structure of JmjC domain of human histone demethylase UTY in complex with fumarate · 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 5FXW · PDBe 5FXW · UniProt O14607
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