› 6dmj

X-ray diffraction
1.15Å resolution

A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain

Released:
DOI: 10.2210/pdb6dmj/pdb
PDB entry 6dmj coloured by chain, front view.
PDB entry 6dmj coloured by chain, side view.
PDB entry 6dmj 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

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130112 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bromodomain-containing protein 4 Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 15.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60885 (Residues: 44-168; Coverage: 9%)
Gene names: BRD4, HUNK1
Sequence domains: Bromodomain
Structure domains: Bromodomain-like

Ligands and Environments

1 bound ligand:
Ligand 53W 1 x 53W
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 39.61Å b: 50.27Å c: 57.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.194
Expression system: Escherichia coli

Quick links

Citations

1 review citation

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

1 mention without citation

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
van Zundert et al. (2018)