Research workbench
UBN1 peptide bound to H3.3/H4/ASF1
Analyse UBN1 peptide bound to H3.3/H4/ASF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZBJ
- Type
- protein
- Length
- 337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone chaperone ASF1; Histone H3; Histone H4; Ubinuclein-1
- UniProt
- P32447, Q10453, P62799, Q9NPG3
- Ligands
- ACE, CL
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone chaperone ASF1 | protein | 160 | 9% helix, 48% strand | P32447 |
| B | Histone H3 | protein | 74 | 72% helix, 3% strand | Q10453 |
| C | Histone H4 | protein | 82 | 61% helix, 7% strand | P62799 |
| D | Ubinuclein-1 | protein | 21 | 24% helix, 5% strand | Q9NPG3 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains D
- CL · Chloride ion · ion · 8 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.51 | 0.76 | 26 | empty |
| 2 | 69 | 0.28 | 0.72 | 17 | CL |
Interfaces
5 interfaces between chains.
- B–C · 2126 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 922 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 766 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 503 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ZBJ · UBN1 peptide bound to H3.3/H4/Asf1 · the same entry in another collection · chain C against C, TM-score 1.00
- P32447 · AlphaFold monomer V2.0 prediction for histone chaperone ASF1 (P32447) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q10453 · AlphaFold monomer V2.0 prediction for histone H3.3 type 1 (Q10453) · a predicted model of the same protein · chain B against A, TM-score 0.91
- Q9NPG3 · AlphaFold monomer V2.0 prediction for ubinuclein-1 (Q9NPG3) · a predicted model of the same protein · chain D against A, TM-score 0.29
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 P32447
- Every structure of UniProt Q10453
- Every structure of UniProt P62799
- Every structure of UniProt Q9NPG3
- Elsewhere: RCSB PDB 4ZBJ · PDBe 4ZBJ · UniProt P32447 · UniProt Q10453 · UniProt P62799 · UniProt Q9NPG3
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