MolNFT v1 · #165662 · protein
Braf dimer bound to 14-3-3
6U2H · 14-3-3 protein ZETA/DELTA: “Braf dimer bound to 14-3-3”. X-ray diffraction, 1 ligand (29L), 17 pockets (best druggability 0.79). MolNFT v1 #165662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U2H
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- 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
- 29L
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein ZETA/DELTA | protein | 230 | 82% helix, 0% strand | P63104 |
| B | 14-3-3 protein ZETA/DELTA | protein | 223 | 82% helix, 0% strand | P63104 |
| C | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 275 | 39% helix, 16% strand | P15056 |
| D | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 283 | 36% helix, 16% strand | P15056 |
Ligands and binding sites
- 29L · 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.79 | 0.84 | 69 | 29L |
| 2 | 659 | 0.69 | 0.77 | 60 | empty |
| 3 | 268 | 0.69 | 0.84 | 40 | 29L |
| 4 | 213 | 0.62 | 0.82 | 25 | empty |
| 5 | 159 | 0.57 | 0.82 | 32 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1248 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1071 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 838 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 656 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 651 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6U2H · BRAF dimer bound to 14-3-3 · 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
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 6U2H · PDBe 6U2H · UniProt P63104 · UniProt P15056
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