Research workbench
Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-peg interactions in proteins
Analyse Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FN9
- Type
- protein
- Length
- 452 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
- DW8, BEZ
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 228 | 83% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 224 | 82% helix, 0% strand | P63104 |
Ligands and binding sites
- DW8 · [2-[2-oxidanylidene-2-[[3-[2-[2-[2-[3-oxidanylidene-3-(propylamino) propoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]amino]etho xy]phenyl]phosphonic acid · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.54 | 0.75 | 26 | empty |
| 2 | 241 | 0.51 | 0.75 | 25 | empty |
| 3 | 231 | 0.48 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6FN9 · 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 B 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 6FN9 · PDBe 6FN9 · UniProt P63104
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