MolNFT v1 · #121715 · protein
DPF3B in complex with H3K14AC peptide
5I3L · Zinc finger protein DPF3: “DPF3B in complex with H3K14AC peptide”. X-ray diffraction, 3 ligands (ZN, NA, UNX), 4 pockets (best druggability 0.58). MolNFT v1 #121715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I3L
- Type
- protein
- Length
- 243 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger protein DPF3; H3K14AC peptide
- UniProt
- Q92784
- Ligands
- ZN, NA, UNX
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger protein DPF3 | protein | 112 | 11% helix, 12% strand | Q92784 |
| B | Zinc finger protein DPF3 | protein | 114 | 15% helix, 10% strand | Q92784 |
| C | H3K14AC peptide | protein | 17 | 47% helix, 12% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · chains B
- UNX · Unknown atom or ion · ion · 32 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.58 | 0.77 | 43 | UNX |
| 2 | 222 | 0.57 | 0.79 | 35 | EDO, UNX |
| 3 | 206 | 0.50 | 0.76 | 40 | UNX |
| 4 | 61 | 0.33 | 0.76 | 14 | UNX |
Interfaces
3 interfaces between chains.
- A–C · 918 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 864 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
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
- Elsewhere: RCSB PDB 5I3L · PDBe 5I3L · UniProt Q92784
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