MolNFT v1 · #182052 · protein
Autoinhibited BRAF:(14-3-3)2:MEK complex with the braf rbd resolved
7MFD · SERINE/THREONINE-protein kinase B-RAF: “Autoinhibited BRAF:(14-3-3)2:MEK complex with the braf rbd resolved”. Electron microscopy, 2 ligands (CHU, ZN), 17 pockets (best druggability 0.86). MolNFT v1 #182052 on GenesisL1: 3D…
- PDB
- 7MFD
- Type
- protein
- Length
- 1,147 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase B-RAF; Dual specificity mitogen-activated protein kinase…
- EC
- 2.7.11.1, 2.7.12.2
- UniProt
- P15056, Q02750, P63104
- Ligands
- CHU, ZN
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 410 | 25% helix, 14% strand | P15056 |
| B | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 293 | 35% helix, 14% strand | Q02750 |
| C | 14-3-3 protein ZETA/DELTA | protein | 220 | 81% helix, 0% strand | P63104 |
| D | 14-3-3 protein ZETA/DELTA | protein | 224 | 79% helix, 0% strand | P63104 |
Ligands and binding sites
- CHU · N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.86 | 0.87 | 131 | ZN |
| 2 | 470 | 0.83 | 0.90 | 71 | CHU |
| 3 | 511 | 0.82 | 0.88 | 71 | empty |
| 4 | 75 | 0.74 | 0.97 | 22 | empty |
| 5 | 743 | 0.74 | 0.79 | 72 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1766 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1372 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1009 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7MFD · Autoinhibited BRAF:(14-3-3)2:MEK complex with the BRAF RBD resolved · 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 D 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 0.64
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 P15056
- Every structure of UniProt Q02750
- Every structure of UniProt P63104
- Elsewhere: RCSB PDB 7MFD · PDBe 7MFD · UniProt P15056 · UniProt Q02750 · UniProt P63104
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