› 6dmk

X-ray diffraction
1.66Å resolution

A multiconformer ligand model of an isoxazolyl-benzimidazole ligand bound to the bromodomain of human CREBBP

Released:
DOI: 10.2210/pdb6dmk/pdb
PDB entry 6dmk coloured by chain, front view.
PDB entry 6dmk coloured by chain, side view.
PDB entry 6dmk 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: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187751 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
CREB-binding protein Chain: A
Molecule details ›
Chain: A
Length: 113 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92793 (Residues: 1083-1195; Coverage: 5%)
Gene names: CBP, CREBBP
Sequence domains: Bromodomain
Structure domains: Bromodomain-like

Ligands and Environments

3 bound ligands:
Ligand NO3 1 x NO3
Ligand 2LL 1 x 2LL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 24.697Å b: 44.311Å c: 52.916Å
α: 90° β: 95.87° γ: 90°
R-values:
R R work R free
0.202 0.2 0.234
Expression system: Escherichia coli BL21(DE3)

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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)