MolNFT v1 · #86758 · protein
14-3-3 interaction with RND3 prenyl-phosphorylation motif
4BG6 · 14-3-3 protein ZETA/DELTA: “14-3-3 interaction with RND3 prenyl-phosphorylation motif”. X-ray diffraction, 1 ligand (FAR), 4 pockets (best druggability 0.55). MolNFT v1 #86758 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4BG6
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; Rho-related GTP-binding protein rhoe
- UniProt
- P63104, P61587
- Ligands
- FAR
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 228 | 82% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 229 | 83% helix, 0% strand | P63104 |
| Q, R | Rho-related GTP-binding protein rhoe | protein | 7 | 0% helix, 0% strand | P61587 |
Ligands and binding sites
- FAR · Farnesyl · ligand · 2 copies · chains A, Q, B, R
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · 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 | 192 | 0.55 | 0.79 | 27 | FAR |
| 2 | 304 | 0.52 | 0.75 | 25 | PE4 |
| 3 | 172 | 0.51 | 0.78 | 23 | FAR |
| 4 | 63 | 0.35 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 900 Ų buried · 14 hydrogen bonds · protein-protein
- A–Q · 604 Ų buried · 14 hydrogen bonds · protein-protein
- B–R · 508 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 2 modified (farnesylation, phosphorylation).
Compared structures
- 4BG6 · 14-3-3 interaction with Rnd3 prenyl-phosphorylation motif · 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
- P61587 · AlphaFold monomer V2.0 prediction for rho-related GTP-binding protein rhoe (P61587) · a predicted model of the same protein · chain Q against A, TM-score 0.58
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 P61587
- Elsewhere: RCSB PDB 4BG6 · PDBe 4BG6 · UniProt P63104 · UniProt P61587
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