MolNFT v1 · #118282 · protein
Small-molecule stabilization of the 14-3-3/GAB2 ppi interface
5EXA · 14-3-3 protein ZETA/DELTA: “Small-molecule stabilization of the 14-3-3/GAB2 ppi interface”. X-ray diffraction, 3 ligands (5SO, BEZ, MG), 4 pockets (best druggability 0.62). MolNFT v1 #118282 on GenesisL1: 3D structure, binding sites…
- PDB
- 5EXA
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; GRB2-associated-binding protein 2
- UniProt
- P63104, Q9UQC2
- Ligands
- 5SO, BEZ, MG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 229 | 83% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 230 | 83% helix, 0% strand | P63104 |
| C | GRB2-associated-binding protein 2 | protein | 9 | 0% helix, 0% strand | Q9UQC2 |
| D | GRB2-associated-binding protein 2 | protein | 11 | 0% helix, 0% strand | Q9UQC2 |
Ligands and binding sites
- 5SO · Fusicoccin A-THF derivative · ligand · 2 copies · chains A, D, B, C
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains 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 | 465 | 0.62 | 0.76 | 30 | empty |
| 2 | 222 | 0.60 | 0.81 | 26 | 5SO |
| 3 | 230 | 0.59 | 0.80 | 28 | 5SO |
| 4 | 53 | 0.31 | 0.76 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–B · 972 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 699 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5EXA · Small-molecule stabilization of the 14-3-3/Gab2 PPI interface · the same entry in another collection · chain D against D, 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
- Q9UQC2 · AlphaFold monomer V2.0 prediction for GRB2-associated-binding protein 2 (Q9UQC2) · a predicted model of the same protein · chain C against A, TM-score 0.43
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
- Every structure of UniProt Q9UQC2
- Elsewhere: RCSB PDB 5EXA · PDBe 5EXA · UniProt P63104 · UniProt Q9UQC2
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