Research workbench
Crystal structure of KSR2:MEK1 in complex with AMP-pnp, and allosteric MEK inhibitor PD0325901
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
- 7JUU
- Type
- protein
- Length
- 579 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, 4BM, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% 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, 19% strand | Q6VAB6 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 302 | 46% helix, 16% strand | P29678 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, C
- 4BM · N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.80 | 0.86 | 62 | 4BM, MG |
| 2 | 304 | 0.76 | 0.88 | 33 | ANP, MG |
| 3 | 361 | 0.62 | 0.78 | 39 | empty |
| 4 | 67 | 0.62 | 0.92 | 22 | empty |
| 5 | 90 | 0.57 | 0.86 | 19 | ANP |
Interfaces
1 interface between chains.
- B–C · 1152 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7JUU · 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 0.95
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 Q6VAB6
- Every structure of UniProt P29678
- Elsewhere: RCSB PDB 7JUU · PDBe 7JUU · UniProt Q6VAB6 · UniProt P29678
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