MolNFT v1 · #150090 · protein
ERK2 signalling protein
6GJD · Mitogen-activated protein kinase 1: “ERK2 signalling protein”. X-ray diffraction, 2 ligands (F0E, SO4), 3 pockets (best druggability 0.70). MolNFT v1 #150090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GJD
- Type
- protein
- Length
- 342 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
- P28482
- Ligands
- F0E, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 342 | 41% helix, 16% strand | P28482 |
Ligands and binding sites
- F0E · cyclooctyl ~{N}-[3-[[4-[5-[[(3~{R})-1-[2-oxidanylidene-2-[4-(4-pyrimidin-2-ylphenyl)piperazin-1-yl]ethyl]pyrrolidin-3-yl]carbonylamino]-1~{H}-indazol-3-yl]pyridin-2-yl]carbonylamino]propyl]carbamate · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- GOL · Glycerol · additive · 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 | 415 | 0.70 | 0.81 | 37 | DMS, F0E |
| 2 | 139 | 0.52 | 0.80 | 29 | empty |
| 3 | 105 | 0.44 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6GJD · Erk2 signalling protein · 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
- Elsewhere: RCSB PDB 6GJD · PDBe 6GJD · UniProt P28482
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