MolNFT v1 · #149241 · protein
Crystal structure of utx complexed with 5-hydroxy-4-keto-1-methyl- picolinate
6FUL · Lysine-specific demethylase 6A: “Crystal structure of utx complexed with 5-hydroxy-4-keto-1-methyl- picolinate”. X-ray diffraction, 4 ligands (E7Z, MN, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #149241 on GenesisL1: 3D…
- PDB
- 6FUL
- Type
- protein
- Length
- 478 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
- E7Z, MN, ZN, SO4
- Pockets
- 5 · best druggability 0.73
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 | 478 | 35% helix, 22% strand | O15550 |
Ligands and binding sites
- E7Z · 1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 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 | 573 | 0.73 | 0.81 | 45 | E7Z, MN |
| 2 | 460 | 0.65 | 0.78 | 53 | SO4 |
| 3 | 62 | 0.35 | 0.77 | 15 | empty |
| 4 | 72 | 0.33 | 0.75 | 12 | empty |
| 5 | 53 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 6FUL · Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate · 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 6FUL · PDBe 6FUL · UniProt O15550
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