MolNFT v1 · #58192 · protein
Catalytic fragment of UTX/KDM6A bound with histone H3K27ME3 peptide, N-oxyalylglycine, and NI(II)
3AVR · Lysine-specific demethylase 6A: “Catalytic fragment of UTX/KDM6A bound with histone H3K27ME3 peptide, N-oxyalylglycine, and NI(II)”. X-ray diffraction, 4 ligands (OGA, ZN, NI), 5 pockets (best druggability 0.74). MolNFT v1 #58192 on…
- PDB
- 3AVR
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6A; Histone H3
- EC
- 1.14.11.-
- UniProt
- O15550
- Ligands
- OGA, ZN, NI, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6A (EC 1.14.11.-) | protein | 473 | 34% helix, 23% strand | O15550 |
| B | Histone H3 | protein | 17 | 0% helix, 18% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.74 | 0.87 | 44 | OGA, NI |
| 2 | 493 | 0.67 | 0.78 | 48 | EDO |
| 3 | 61 | 0.42 | 0.82 | 20 | empty |
| 4 | 84 | 0.33 | 0.74 | 21 | empty |
| 5 | 58 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1310 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3AVR · Catalytic fragment of UTX/KDM6A bound with histone H3K27me3 peptide, N-oxyalylglycine… · the same entry in another collection · chain A against A, TM-score 1.00
- O15550 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6A (O15550) · a predicted model of the same protein · chain A 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 O15550
- Elsewhere: RCSB PDB 3AVR · PDBe 3AVR · UniProt O15550
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.