MolNFT v1 · #190929 · protein
Crystal structure of YTHDF2 with compound YLI_DC1_005
7Z7F · Yth domain-containing family protein 2: “Crystal structure of YTHDF2 with compound YLI_DC1_005”. X-ray diffraction, 3 ligands (IF3, SO4, CL), 3 pockets (best druggability 0.51). MolNFT v1 #190929 on GenesisL1: 3D structure, binding…
- PDB
- 7Z7F
- Type
- protein
- Length
- 298 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
- IF3, SO4, CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yth domain-containing family protein 2 | protein | 149 | 29% helix, 30% strand | Q9Y5A9 |
Ligands and binding sites
- IF3 · ~{N}2,~{N}6,9-trimethylpurine-2,6-diamine · ligand · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
- 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 | 91 | 0.51 | 0.83 | 26 | IF3 |
| 2 | 51 | 0.43 | 0.83 | 14 | empty |
| 3 | 81 | 0.40 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 441 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7Z7F · Crystal structure of YTHDF2 with compound YLI_DC1_005 · 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 A against A, TM-score 0.95
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 7Z7F · PDBe 7Z7F · UniProt Q9Y5A9
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