Research workbench
Crystal structure of KSR2:MEK1 in complex with AMP-pnp, and allosteric MEK inhibitor trametinib
Analyse Crystal structure of KSR2:MEK1 in complex with AMP-pnp, and allosteric MEK… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JUR
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinase suppressor of RAS 2; Dual specificity mitogen-activated protein kinase kinase 1
- EC
- 2.7.11.1, 2.7.12.2
- UniProt
- Q6VAB6, P29678
- Ligands
- ANP, QOM, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Kinase suppressor of RAS 2 (EC 2.7.11.1) | protein | 277 | 40% helix, 18% strand | Q6VAB6 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 304 | 42% helix, 15% strand | P29678 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, C
- QOM · Trametinib · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.82 | 0.83 | 93 | ANP, QOM |
| 2 | 422 | 0.79 | 0.88 | 52 | ANP, MG |
| 3 | 357 | 0.62 | 0.78 | 39 | empty |
| 4 | 83 | 0.45 | 0.80 | 19 | empty |
| 5 | 86 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- B–C · 1165 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7JUR · Crystal Structure of KSR2:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor… · the same entry in another collection · chain B against B, TM-score 1.00
- P29678 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q6VAB6 · AlphaFold monomer V2.0 prediction for kinase suppressor of RAS 2 (Q6VAB6) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q6VAB6
- Every structure of UniProt P29678
- Elsewhere: RCSB PDB 7JUR · PDBe 7JUR · UniProt Q6VAB6 · UniProt P29678
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