MolNFT v1 · #93674 · protein
Complex structure 5 of DAXX(E225A)/H3.3(SUB5,G90A)/H4
4H9R · Histone H3.3: “Complex structure 5 of DAXX(E225A)/H3.3(SUB5,G90A)/H4”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.75). MolNFT v1 #93674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4H9R
- 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 0.75
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 | 63% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 83 | 54% helix, 4% strand | P62805 |
| C | Death domain-associated protein 6 | protein | 205 | 71% helix, 1% strand | Q9UER7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.75 | 0.89 | 31 | empty |
| 2 | 70 | 0.74 | 0.98 | 25 | empty |
| 3 | 94 | 0.36 | 0.74 | 20 | empty |
| 4 | 62 | 0.29 | 0.74 | 12 | PO4 |
Interfaces
3 interfaces between chains.
- A–C · 3175 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2110 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1768 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4H9R · Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/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 4H9R · PDBe 4H9R · UniProt P84243 · UniProt P62805 · UniProt Q9UER7
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