MolNFT v1 · #132683 · protein
Xchem group deposition -- crystal structure of human YEATS4 in complex with FM000199E
5R68 · Yeats domain-containing protein 4: “Xchem group deposition -- crystal structure of human YEATS4 in complex with FM000199E”. X-ray diffraction, 1 ligand (RYD), 2 pockets (best druggability 0.67). MolNFT v1 #132683 on GenesisL1: 3D…
- PDB
- 5R68
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeats domain-containing protein 4
- UniProt
- O95619
- Ligands
- RYD
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Yeats domain-containing protein 4 | protein | 131 | 8% helix, 52% strand | O95619 |
| A | Yeats domain-containing protein 4 | protein | 130 | 8% helix, 52% strand | O95619 |
Ligands and binding sites
- RYD · (1-methylbenzotriazol-5-yl)methanol · ligand · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.67 | 0.76 | 60 | EDO |
| 2 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 655 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5R68 · XChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e · the same entry in another collection · chain B against B, TM-score 1.00
- O95619 · AlphaFold monomer V2.0 prediction for yeats domain-containing protein 4 (O95619) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O95619
- Elsewhere: RCSB PDB 5R68 · PDBe 5R68 · UniProt O95619
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