MolNFT v1 · #190926 · protein
Crystal structure of YTHDF2 with compound YLI_DC1_003
7Z7B · Yth domain-containing family protein 2: “Crystal structure of YTHDF2 with compound YLI_DC1_003”. X-ray diffraction, 3 ligands (OYK, SO4, CL), 2 pockets (best druggability 0.49). MolNFT v1 #190926 on GenesisL1: 3D structure, binding…
- PDB
- 7Z7B
- Type
- protein
- Length
- 297 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
- OYK, SO4, CL
- Pockets
- 2 · best druggability 0.49
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 | 149 | 29% helix, 30% strand | Q9Y5A9 |
| B | Yth domain-containing family protein 2 | protein | 148 | 29% helix, 30% strand | Q9Y5A9 |
Ligands and binding sites
- OYK · ~{N},9-dimethylpurin-6-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.49 | 0.84 | 21 | CL, OYK |
| 2 | 62 | 0.43 | 0.82 | 20 | OYK |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7Z7B · Crystal structure of YTHDF2 with compound YLI_DC1_003 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 7Z7B · PDBe 7Z7B · UniProt Q9Y5A9
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