Research workbench
Crystal structure of KSR1:MEK1 in complex with AMP-pnp, and allosteric MEK inhibitor cobimetinib
Analyse Crystal structure of KSR1: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
- 7JUY
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinase suppressor of RAS 1; Dual specificity mitogen-activated protein kinase kinase 1
- EC
- 2.7.11.1, 2.7.12.2
- UniProt
- Q8IVT5, P29678
- Ligands
- ANP, EUI, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Kinase suppressor of RAS 1 (EC 2.7.11.1) | protein | 276 | 42% helix, 18% strand | Q8IVT5 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 311 | 47% helix, 17% strand | P29678 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, C
- EUI · [3,4-bis(fluoranyl)-2-[(2-fluoranyl-4-iodanyl-phenyl) amino]phenyl]-[3-oxidanyl-3-[(2S)-piperidin-2-yl]azetidin-1-yl]methanone · ligand · chains 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 | 710 | 0.81 | 0.85 | 70 | ANP, EUI, MG |
| 2 | 636 | 0.72 | 0.79 | 77 | ANP, MG |
| 3 | 197 | 0.53 | 0.78 | 24 | empty |
| 4 | 122 | 0.44 | 0.77 | 22 | empty |
| 5 | 83 | 0.43 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- B–C · 1065 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7JUY · Crystal Structure of KSR1: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
- Q8IVT5 · AlphaFold monomer V2.0 prediction for kinase suppressor of RAS 1 (Q8IVT5) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q8IVT5
- Every structure of UniProt P29678
- Elsewhere: RCSB PDB 7JUY · PDBe 7JUY · UniProt Q8IVT5 · UniProt P29678
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