Research workbench
Xchem group deposition -- crystal structure of human YEATS4 in complex with XS038644E
Analyse Xchem group deposition -- crystal structure of human YEATS4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5R69
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeats domain-containing protein 4
- UniProt
- O95619
- Ligands
- ZHA
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Yeats domain-containing protein 4 | protein | 130 | 8% helix, 52% strand | O95619 |
| A | Yeats domain-containing protein 4 | protein | 135 | 10% helix, 50% strand | O95619 |
Ligands and binding sites
- ZHA · ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide · ligand · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.62 | 0.75 | 49 | EDO |
Interfaces
1 interface between chains.
- B–A · 471 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5R69 · XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e · 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 B against A, TM-score 0.97
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 5R69 · PDBe 5R69 · UniProt O95619
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