MolNFT v1 · #119495 · protein
Crystal structure of jmjc domain of human histone demethylase uty in complex with N05859B
5FXV: “Crystal structure of jmjc domain of human histone demethylase uty in complex with N05859B”. X-ray diffraction, 3 ligands (MN1, ZN, MN), 9 pockets (best druggability 0.79). MolNFT v1 #119495 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FXV
- Type
- protein
- Length
- 881 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase uty
- UniProt
- O14607
- Ligands
- MN1, ZN, MN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase uty | protein | 442 | 36% helix, 24% strand | O14607 |
| B | Histone demethylase uty | protein | 439 | 36% helix, 23% strand | O14607 |
Ligands and binding sites
- MN1 · 4-carboxypiperidine · 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 · 10 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 | 1072 | 0.79 | 0.80 | 102 | empty |
| 2 | 531 | 0.72 | 0.81 | 47 | MN, MN1 |
| 3 | 471 | 0.70 | 0.81 | 45 | MN, MN1 |
| 4 | 244 | 0.59 | 0.79 | 25 | empty |
| 5 | 57 | 0.45 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1068 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5FXV · Crystal structure of JmjC domain of human histone demethylase UTY in complex with N05859b · 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 5FXV · PDBe 5FXV · UniProt O14607
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