Research workbench
Crystal structure of ERK2 in complex with an adenosine derivative
Analyse Crystal structure of ERK2 in complex with an adenosine derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FI3
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1
- EC
- 2.7.11.24
- UniProt
- P63086
- Ligands
- DJ2, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 338 | 40% helix, 15% strand | P63086 |
Ligands and binding sites
- DJ2 · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(azanyloxymethyl)oxolane-3,4-diol · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.69 | 0.79 | 44 | DJ2 |
| 2 | 116 | 0.54 | 0.82 | 27 | empty |
| 3 | 62 | 0.29 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6FI3 · Crystal structure of ERK2 in complex with an adenosine derivative · the same entry in another collection · chain A against A, 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 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 P63086
- Elsewhere: RCSB PDB 6FI3 · PDBe 6FI3 · UniProt P63086
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