Research workbench
Crystal structure of KSR1:MEK1 in complex with AMP-pnp, and allosteric MEK inhibitor aps-9-95-1
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
- 7JV1
- Type
- protein
- Length
- 583 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, VKG, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Kinase suppressor of RAS 1 (EC 2.7.11.1) | protein | 275 | 42% helix, 17% strand | Q8IVT5 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 308 | 45% helix, 15% strand | P29678 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains D, C
- VKG · N-(3-{3-cyclopropyl-5-[(2-fluoro-4-iodophenyl)amino]-6, 8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin-1(2H)-yl}phenyl)-N'-methylsulfuric diamide · ligand · chains D, C
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.84 | 92 | ANP, VKG |
| 2 | 353 | 0.66 | 0.80 | 46 | ANP, MG |
| 3 | 433 | 0.63 | 0.77 | 43 | empty |
| 4 | 65 | 0.58 | 0.89 | 12 | empty |
| 5 | 86 | 0.47 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- D–C · 987 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7JV1 · Crystal Structure of KSR1:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor… · the same entry in another collection · chain D against D, 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 0.96
- Q8IVT5 · AlphaFold monomer V2.0 prediction for kinase suppressor of RAS 1 (Q8IVT5) · a predicted model of the same protein · chain D 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 7JV1 · PDBe 7JV1 · UniProt Q8IVT5 · UniProt P29678
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