Research workbench
Crystal structure of ERK2 in complex with N-cyclohexyl-9H-purin-6-amine
Analyse Crystal structure of ERK2 in complex with N-cyclohexyl-9H-purin-6-amine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QP1
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Mitogen-activated protein kinase 1
- EC
- 2.7.11.24
- UniProt
- P28482
- Ligands
- EMU
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 343 | 38% helix, 13% strand | P28482 |
| B | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 344 | 34% helix, 12% strand | P28482 |
Ligands and binding sites
- EMU · N-benzyl-9H-purin-6-amine · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.78 | 0.80 | 110 | EMU, IMD |
| 2 | 195 | 0.69 | 0.86 | 21 | empty |
| 3 | 349 | 0.66 | 0.80 | 37 | EMU, IMD |
| 4 | 297 | 0.52 | 0.74 | 39 | empty |
| 5 | 132 | 0.49 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4QP1 · Crystal structure of ERK2 in complex with N-cyclohexyl-9H-purin-6- amine · the same entry in another collection · chain A against A, TM-score 1.00
- P28482 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 1 (P28482) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P28482
- Elsewhere: RCSB PDB 4QP1 · PDBe 4QP1 · UniProt P28482
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