MolNFT v1 · #58193 · protein
Catalytic fragment of UTX/KDM6A bound with N-oxyalylglycine, and NI(II)
3AVS · Lysine-specific demethylase 6A: “Catalytic fragment of UTX/KDM6A bound with N-oxyalylglycine, and NI(II)”. X-ray diffraction, 4 ligands (OGA, NI, ZN), 4 pockets (best druggability 0.71). MolNFT v1 #58193 on GenesisL1: 3D structure…
- PDB
- 3AVS
- Type
- protein
- Length
- 474 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6A
- EC
- 1.14.11.-
- UniProt
- O15550
- Ligands
- OGA, NI, ZN, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6A (EC 1.14.11.-) | protein | 474 | 35% helix, 22% strand | O15550 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- NI · Nickel (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.71 | 0.80 | 49 | OGA, NI |
| 2 | 499 | 0.67 | 0.78 | 53 | EDO |
| 3 | 82 | 0.40 | 0.78 | 20 | empty |
| 4 | 71 | 0.33 | 0.75 | 12 | empty |
Compared structures
- 3AVS · Catalytic fragment of UTX/KDM6A bound with N-oxyalylglycine, and Ni(II) · 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 1.00
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 3AVS · PDBe 3AVS · UniProt O15550
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