Research workbench
Crystal structure of human ERK2 complexed with a MAPK docking peptide
Analyse Crystal structure of human ERK2 complexed with a MAPK docking peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H3P
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1; Ribosomal protein S6 kinase alpha-1
- EC
- 2.7.11.24, 2.7.11.1
- UniProt
- P28482, Q15418
- Ligands
- ANP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 342 | 35% helix, 15% strand | P28482 |
| D | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 338 | 36% helix, 16% strand | P28482 |
| B | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 16 | 44% helix, 0% strand | Q15418 |
| E | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 17 | 41% helix, 0% strand | Q15418 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.74 | 0.78 | 74 | ANP |
| 2 | 461 | 0.72 | 0.82 | 42 | ANP |
| 3 | 103 | 0.55 | 0.84 | 23 | empty |
| 4 | 327 | 0.55 | 0.75 | 41 | empty |
| 5 | 147 | 0.49 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- D–E · 763 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 745 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4H3P · Crystal structure of human ERK2 complexed with a MAPK docking peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain B against A, TM-score 0.49
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
- Every structure of UniProt Q15418
- Elsewhere: RCSB PDB 4H3P · PDBe 4H3P · UniProt P28482 · UniProt Q15418
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