Research workbench
Crystal structure of the BRAF:MEK1 kinases in complex with amppnp and trametinib
Analyse Crystal structure of the BRAF:MEK1 kinases in complex with amppnp and trametinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M0Y
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- 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
- Ligands
- ANP, QOM, MG, SO4
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 275 | 38% helix, 16% strand | P15056 |
| B | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 308 | 45% helix, 16% strand | Q02750 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- QOM · Trametinib · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
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 | 1198 | 0.86 | 0.87 | 122 | ANP, MG, SO4, QOM |
| 2 | 302 | 0.60 | 0.78 | 40 | empty |
| 3 | 66 | 0.47 | 0.84 | 17 | empty |
| 4 | 82 | 0.43 | 0.80 | 16 | empty |
| 5 | 98 | 0.38 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1352 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7M0Y · Crystal structure of the BRAF:MEK1 kinases in complex with AMPPNP and Trametinib · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.95
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
- Elsewhere: RCSB PDB 7M0Y · PDBe 7M0Y · UniProt P15056 · UniProt Q02750
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