MolNFT v1 · #82720 · protein
X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and mgatp
3VVH · Dual specificity mitogen-activated protein kinase kinase 1: “X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor…”. X-ray diffraction, 3 ligands (ATP, 4BM, MG), 9 pockets (best…
- PDB
- 3VVH
- Type
- protein
- Length
- 860 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity mitogen-activated protein kinase kinase 1
- EC
- 2.7.12.2
- UniProt
- Q02750
- Ligands
- ATP, 4BM, MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 287 | 44% helix, 17% strand | Q02750 |
| B | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 290 | 45% helix, 17% strand | Q02750 |
| C | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 283 | 44% helix, 17% strand | Q02750 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- 4BM · N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, 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 | 677 | 0.82 | 0.86 | 65 | MG, ATP, 4BM |
| 2 | 705 | 0.81 | 0.85 | 73 | MG, ATP, 4BM |
| 3 | 650 | 0.75 | 0.81 | 61 | MG, ATP, 4BM |
| 4 | 535 | 0.68 | 0.78 | 50 | empty |
| 5 | 450 | 0.65 | 0.78 | 46 | empty |
Interfaces
2 interfaces between chains.
- A–C · 434 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3VVH · X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02750 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q02750
- Elsewhere: RCSB PDB 3VVH · PDBe 3VVH · UniProt Q02750
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