Research workbench
KSR2:MEK1 complex bound to the small molecule aps-2-79
Analyse KSR2:MEK1 complex bound to the small molecule aps-2-79 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKR
- 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
- 6U7
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Kinase suppressor of RAS 2 (EC 2.7.11.1) | protein | 272 | 31% helix, 11% strand | Q6VAB6 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 309 | 39% helix, 12% strand | P29678 |
Ligands and binding sites
- 6U7 · 6,7-dimethoxy-~{N}-(2-methyl-4-phenoxy-phenyl) quinazolin-4-amine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.81 | 0.82 | 84 | empty |
| 2 | 312 | 0.66 | 0.81 | 30 | 6U7 |
| 3 | 268 | 0.55 | 0.76 | 33 | empty |
| 4 | 180 | 0.52 | 0.78 | 28 | empty |
| 5 | 72 | 0.52 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- B–C · 1013 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KKR · KSR2:MEK1 Complex Bound to the Small Molecule APS-2-79 · 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 0.97
- 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 0.93
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 Q6VAB6
- Every structure of UniProt P29678
- Elsewhere: RCSB PDB 5KKR · PDBe 5KKR · UniProt Q6VAB6 · UniProt P29678
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