› 6dmg

X-ray diffraction
2.2Å resolution

A multiconformer ligand model of EK6 bound to ERK2

Released:
DOI: 10.2210/pdb6dmg/pdb
PDB entry 6dmg coloured by chain, front view.
PDB entry 6dmg coloured by chain, side view.
PDB entry 6dmg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H
J Med Chem 61 11183-11198 (2018)
PMID: 30457858

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mitogen-activated protein kinase 1 Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 40.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P28482 (Residues: 11-357; Coverage: 96%)
Gene names: ERK2, MAPK1, PRKM1, PRKM2
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 3 x SO4
Ligand EDO 3 x EDO
Ligand EK6 1 x EK6
1 modified residue:
Ligand CME 1 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 48.78Å b: 70.7Å c: 60.86Å
α: 90° β: 110.11° γ: 90°
R-values:
R R work R free
0.189 0.186 0.236
Expression system: Escherichia coli

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Citations

1 review citation

Advances in methods for atomic resolution macromolecular structure determination.
Thompson et al. (2020)
24 other articles

3 mentions without citation

MGRA: Motion Gesture Recognition via Accelerometer.
Hong et al. (2016)
2 more