MolNFT v1 · #190779 · protein
Crystal structure of YTHDF2 with compound ZA_143
7YXE · Yth domain-containing family protein 2: “Crystal structure of YTHDF2 with compound ZA_143”. X-ray diffraction, 3 ligands (I82, NA, SO4), 3 pockets (best druggability 0.50). MolNFT v1 #190779 on GenesisL1: 3D structure, binding sites…
- PDB
- 7YXE
- Type
- protein
- Length
- 296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing family protein 2
- UniProt
- Q9Y5A9
- Ligands
- I82, NA, SO4
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing family protein 2 | protein | 148 | 29% helix, 30% strand | Q9Y5A9 |
| B | Yth domain-containing family protein 2 | protein | 148 | 29% helix, 30% strand | Q9Y5A9 |
Ligands and binding sites
- I82 · ~{N}-methyl-3-phenyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.50 | 0.84 | 26 | I82 |
| 2 | 75 | 0.46 | 0.82 | 22 | I82 |
| 3 | 53 | 0.43 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 431 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 Q9Y5A9
- Elsewhere: RCSB PDB 7YXE · PDBe 7YXE · UniProt Q9Y5A9
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