MolNFT v1 · #149005 · protein
Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-peg interactions in proteins
6FNB · 14-3-3 protein ZETA/DELTA: “Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-peg interactions in proteins”. X-ray diffraction, 4 ligands (BEZ, DWQ, CA), 4 pockets (best druggability 0.55). MolNFT v1…
- PDB
- 6FNB
- Type
- protein
- Length
- 457 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA
- UniProt
- P63104
- Ligands
- BEZ, DWQ, CA, CL
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 228 | 84% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 229 | 80% helix, 0% strand | P63104 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- DWQ · [2-[2-oxidanylidene-2-[[3-[2-[5-[3-oxidanylidene-3-[3-[2-[2-[3-[3-[2-[2-[2-[[3-[2-(2-phosphonophenoxy) ethanoylamino]phenyl]carbonylamino]ethoxy]ethoxy]ethox y]propanoylamino]propoxy]ethoxy]ethoxy]propylamino]pro poxy]pentoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl ]phosphonic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.55 | 0.75 | 26 | CA, CL |
| 2 | 282 | 0.54 | 0.75 | 30 | DWQ |
| 3 | 279 | 0.50 | 0.74 | 31 | empty |
| 4 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6FNB · Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG… · the same entry in another collection · chain A against A, TM-score 1.00
- P63104 · AlphaFold monomer V2.0 prediction for 14-3-3 protein ZETA/DELTA (P63104) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P63104
- Elsewhere: RCSB PDB 6FNB · PDBe 6FNB · UniProt P63104
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