MolNFT v1 · #72859 · protein
Impaired binding of 14-3-3 to RAF1 is linked to noonan and leopard syndrome
3NKX · 14-3-3 protein ZETA/DELTA: “Impaired binding of 14-3-3 to RAF1 is linked to noonan and leopard syndrome”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #72859 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3NKX
- Type
- protein
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; Peptide of RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- P63104, P04049
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 229 | 82% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 228 | 79% helix, 0% strand | P63104 |
| P | Peptide of RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 9 | 0% helix, 0% strand | P04049 |
| Q | Peptide of RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 8 | 0% helix, 0% strand | P04049 |
Ligands and binding sites
- PPI · Propanoic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.69 | 0.87 | 27 | empty |
| 2 | 171 | 0.67 | 0.86 | 28 | empty |
| 3 | 280 | 0.49 | 0.74 | 25 | empty |
| 4 | 55 | 0.36 | 0.79 | 16 | empty |
| 5 | 53 | 0.33 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 963 Ų buried · 12 hydrogen bonds · protein-protein
- A–P · 748 Ų buried · 18 hydrogen bonds · protein-protein
- B–Q · 667 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3NKX · Impaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPARD syndrome · the same entry in another collection · chain Q against Q, 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
- P04049 · AlphaFold monomer V2.0 prediction for RAF proto-oncogene SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain Q against A, TM-score 0.63
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 P04049
- Elsewhere: RCSB PDB 3NKX · PDBe 3NKX · UniProt P63104 · UniProt P04049
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