Research workbench
Structural dissection of human mitogen-activated kinase ERK1
Analyse Structural dissection of human mitogen-activated kinase ERK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZOQ
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 3
- EC
- 2.7.11.24
- UniProt
- P27361
- Ligands
- 5ID, NA, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mitogen-activated protein kinase 3 (EC 2.7.11.24) | protein | 352 | 38% helix, 14% strand | P27361 |
Ligands and binding sites
- 5ID · (2R,3R,4S,5R)-2-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3, 4-diol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 770 | 0.76 | 0.80 | 92 | empty |
| 2 | 336 | 0.67 | 0.82 | 53 | 5ID, SO4, NA |
| 3 | 231 | 0.64 | 0.82 | 37 | 5ID, NA |
| 4 | 135 | 0.53 | 0.81 | 23 | empty |
| 5 | 79 | 0.42 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1213 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2ZOQ · Structural dissection of human mitogen-activated kinase ERK1 · the same entry in another collection · chain A against A, TM-score 1.00
- P27361 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 3 (P27361) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P27361
- Elsewhere: RCSB PDB 2ZOQ · PDBe 2ZOQ · UniProt P27361
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