Research workbench
Complex structure 1 of DAXX/H3.3(SUB5)/H4
Analyse Complex structure 1 of DAXX/H3.3(SUB5)/H4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H9N
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Death domain-associated protein 6
- UniProt
- P84243, P62805, Q9UER7
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.3 | protein | 98 | 62% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 83 | 55% helix, 4% strand | P62805 |
| C | Death domain-associated protein 6 | protein | 205 | 70% helix, 1% strand | Q9UER7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.74 | 0.98 | 24 | empty |
| 2 | 215 | 0.73 | 0.89 | 26 | empty |
| 3 | 50 | 0.64 | 0.95 | 16 | empty |
| 4 | 103 | 0.38 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3193 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2114 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1776 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4H9N · Complex structure 1 of DAXX/H3.3(sub5)/H4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UER7 · AlphaFold monomer V2.0 prediction for death domain-associated protein 6 (Q9UER7) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P84243
- Every structure of UniProt P62805
- Every structure of UniProt Q9UER7
- Elsewhere: RCSB PDB 4H9N · PDBe 4H9N · UniProt P84243 · UniProt P62805 · UniProt Q9UER7
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