Research workbench
Crystal structure of AF9 yeats domain in complex with H4K5ACK8AC peptide
Analyse Crystal structure of AF9 yeats domain in complex with H4K5ACK8AC peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EIC
- Type
- protein
- Length
- 278 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H4; Protein af-9
- UniProt
- P62805, P42568
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Histone H4 | protein | 9 | 0% helix, 22% strand | P62805 |
| A | Protein af-9 | protein | 138 | 11% helix, 51% strand | P42568 |
| B | Protein af-9 | protein | 131 | 9% helix, 51% strand | P42568 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.45 | 0.82 | 16 | empty |
| 2 | 133 | 0.43 | 0.76 | 24 | empty |
| 3 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 513 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 442 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 7EIC · Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide · the same entry in another collection · chain C against C, TM-score 1.00
- P42568 · AlphaFold monomer V2.0 prediction for protein af-9 (P42568) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain C against A, TM-score 0.32
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 P62805
- Every structure of UniProt P42568
- Elsewhere: RCSB PDB 7EIC · PDBe 7EIC · UniProt P62805 · UniProt P42568
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