Research workbench
Crystal structure of ERK2 complex with kim peptide derived from MKP3
Analyse Crystal structure of ERK2 complex with kim peptide derived from MKP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FYS
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1; Dual specificity protein phosphatase 6
- EC
- 2.7.1.37, 3.1.3.48, 3.1.3.16
- UniProt
- P63086, Q64346
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mitogen-activated protein kinase 1 (EC 2.7.1.37) | protein | 338 | 37% helix, 15% strand | P63086 |
| A | Mitogen-activated protein kinase 1 (EC 2.7.1.37) | protein | 348 | 36% helix, 15% strand | P63086 |
| D, C | Dual specificity protein phosphatase 6 (EC 3.1.3.48, 3.1.3.16) | protein | 11 | 0% helix, 0% strand | Q64346 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.75 | 0.79 | 106 | empty |
| 2 | 298 | 0.68 | 0.82 | 33 | empty |
| 3 | 55 | 0.66 | 0.96 | 21 | empty |
| 4 | 270 | 0.59 | 0.79 | 40 | empty |
| 5 | 187 | 0.55 | 0.79 | 28 | empty |
Interfaces
4 interfaces between chains.
- B–A · 856 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 725 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 283 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2FYS · Crystal structure of Erk2 complex with KIM peptide derived from MKP3 · the same entry in another collection · chain C against C, TM-score 1.00
- P63086 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 1 (P63086) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q64346 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 6 (Q64346) · a predicted model of the same protein · chain D against A, TM-score 0.37
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 P63086
- Every structure of UniProt Q64346
- Elsewhere: RCSB PDB 2FYS · PDBe 2FYS · UniProt P63086 · UniProt Q64346
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