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Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide
Analyse Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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