MolNFT v2 · #213159 · protein
Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide
8IIY · Maltodextrin-binding protein,YEATS domain-containing…: “Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide”. X-ray diffraction at 2.15, 1 ligand (GLC), 3 pockets (best druggability 0.71). MolNFT v2…
- PDB
- 8IIY
- Type
- protein
- Length
- 524 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Escherichia coli; Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Maltodextrin-binding protein,YEATS domain-containing protein 4; Histone H3.1
- UniProt
- C3SHQ8, O95619, P68431
- Ligands
- GLC
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.15 · 3 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding protein,YEATS domain-containing protein 4 | protein | 506 | 36% helix, 28% strand | C3SHQ8, O95619 |
| B | Histone H3.1 | protein | 11 | 0% helix, 36% strand | P68431 |
| C | Histone H3.1 | protein | 7 | 0% helix, 14% strand | P68431 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.71 | 0.82 | 38 | GLC |
| 2 | 579 | 0.70 | 0.79 | 51 | empty |
| 3 | 67 | 0.32 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 566 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain C against A, TM-score 0.54
- 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 0.27
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 C3SHQ8
- Every structure of UniProt O95619
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 8IIY · PDBe 8IIY · UniProt C3SHQ8 · UniProt O95619 · UniProt P68431
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