Research workbench
Crystal structure of ERK-2 with hypothemycin covalently bound
Analyse Crystal structure of ERK-2 with hypothemycin covalently bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9W
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- 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
- HMY
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 336 | 39% helix, 15% strand | P63086 |
Ligands and binding sites
- HMY · (1aR,8S,13S,14S,15aR)-5,13,14-trihydroxy-3-methoxy-8-methyl-8,9,13,14,15,15a-hexahydro-6H-oxireno[k][2]benzoxacyclotetradecine-6,12(1aH)-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.64 | 0.79 | 33 | HMY |
| 2 | 273 | 0.61 | 0.79 | 33 | HMY |
| 3 | 63 | 0.41 | 0.80 | 18 | empty |
| 4 | 106 | 0.39 | 0.76 | 23 | empty |
| 5 | 86 | 0.39 | 0.77 | 20 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3C9W · Crystal Structure of ERK-2 with hypothemycin covalently bound · 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 3C9W · PDBe 3C9W · UniProt P63086
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