Research workbench
The structure of the MAP2K MEK6 reveals an autoinhibitory dimer
Analyse The structure of the MAP2K MEK6 reveals an autoinhibitory dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ENM
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity mitogen-activated protein kinase kinase 6
- EC
- 2.7.12.2
- UniProt
- P52564
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) | protein | 279 | 45% helix, 14% strand | P52564 |
| B | Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) | protein | 271 | 43% helix, 13% strand | P52564 |
| C | Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) | protein | 275 | 45% helix, 12% strand | P52564 |
| D | Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) | protein | 282 | 42% helix, 14% strand | P52564 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.70 | 0.78 | 79 | empty |
| 2 | 599 | 0.69 | 0.78 | 59 | SO4 |
| 3 | 488 | 0.65 | 0.77 | 57 | empty |
| 4 | 269 | 0.59 | 0.78 | 28 | EDO |
| 5 | 268 | 0.58 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1985 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 264 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 3ENM · The structure of the MAP2K MEK6 reveals an autoinhibitory dimer · the same entry in another collection · chain D against D, TM-score 1.00
- P52564 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P52564
- Elsewhere: RCSB PDB 3ENM · PDBe 3ENM · UniProt P52564
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