Research workbench
Phosphorylated ERK2 in complex with ORF45
Analyse Phosphorylated ERK2 in complex with ORF45 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPM
- Type
- protein
- Length
- 390 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1; Synthetic ERK2 inhibitor peptide; Protein ORF45
- EC
- 2.7.11.24
- UniProt
- P28482, F5HDE4
- Ligands
- ABU, 08G
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 362 | 40% helix, 15% strand | P28482 |
| B | Synthetic ERK2 inhibitor peptide | protein | 17 | 53% helix, 0% strand | — |
| C | Protein ORF45 | protein | 11 | 0% helix, 0% strand | F5HDE4 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · chains A, B
- 08G · 1-[4-(hydroxymethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1S)-1-phenylethyl]urea · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.68 | 0.81 | 42 | 08G |
| 2 | 53 | 0.53 | 0.88 | 19 | empty |
| 3 | 190 | 0.51 | 0.77 | 33 | empty |
| 4 | 120 | 0.40 | 0.75 | 24 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 673 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 487 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 7OPM · Phosphorylated ERK2 in complex with ORF45 · the same entry in another collection · chain A against A, TM-score 1.00
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 F5HDE4
- Elsewhere: RCSB PDB 7OPM · PDBe 7OPM · UniProt P28482 · UniProt F5HDE4
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