MolNFT v1 · #182054 · protein
Dimeric (BRAF)2:(14-3-3)2 complex bound to SB590885 inhibitor
7MFF · 14-3-3 protein ZETA/DELTA: “Dimeric (BRAF)2:(14-3-3)2 complex bound to SB590885 inhibitor”. Electron microscopy, 1 ligand (215), 12 pockets (best druggability 0.69). MolNFT v1 #182054 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7MFF
- Type
- protein
- Length
- 1,000 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein ZETA/DELTA; SERINE/THREONINE-protein kinase B-RAF
- EC
- 2.7.11.1
- UniProt
- P63104, P15056
- Ligands
- 215
- Pockets
- 12 · best druggability 0.69
Structure
electron microscopy · 4 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 14-3-3 protein ZETA/DELTA | protein | 229 | 83% helix, 0% strand | P63104 |
| D | 14-3-3 protein ZETA/DELTA | protein | 228 | 79% helix, 0% strand | P63104 |
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 271 | 36% helix, 15% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 272 | 35% helix, 14% strand | P15056 |
Ligands and binding sites
- 215 · (1Z)-5-(2-{4-[2-(dimethylamino)ethoxy]phenyl}-5-pyridin-4-yl-1H-imidazol-4-yl)indan-1-one oxime · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.69 | 0.83 | 34 | 215 |
| 2 | 286 | 0.69 | 0.83 | 32 | 215 |
| 3 | 58 | 0.57 | 0.90 | 16 | empty |
| 4 | 198 | 0.56 | 0.79 | 23 | empty |
| 5 | 282 | 0.53 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1126 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 827 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 784 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7MFF · Dimeric (BRAF)2:(14-3-3)2 complex bound to SB590885 Inhibitor · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.98
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P15056
- Elsewhere: RCSB PDB 7MFF · PDBe 7MFF · UniProt P63104 · UniProt P15056
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