Research workbench
Structure of human DPF3 double-phd domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14
Analyse Structure of human DPF3 double-phd domain bound to histone H3 tail peptide with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SZC
- Type
- protein
- Length
- 130 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger protein DPF3; Histone H3 tail peptide
- UniProt
- Q92784, V9H1G0
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger protein DPF3 | protein | 115 | 15% helix, 12% strand | Q92784 |
| H | Histone H3 tail peptide | protein | 15 | 47% helix, 13% strand | V9H1G0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- 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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.50 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–H · 894 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation, methylation).
Compared structures
- 5SZC · Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92784 · AlphaFold monomer V2.0 prediction for zinc finger protein DPF3 (Q92784) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q92784
- Every structure of UniProt V9H1G0
- Elsewhere: RCSB PDB 5SZC · PDBe 5SZC · UniProt Q92784 · UniProt V9H1G0
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