› 6dmh

X-ray diffraction
1.3Å resolution

A multiconformer ligand model of acylenzyme intermediate of meropenem bound to an SFC-1 E166A mutant

Released:
DOI: 10.2210/pdb6dmh/pdb
PDB entry 6dmh coloured by chain, front view.
PDB entry 6dmh coloured by chain, side view.
PDB entry 6dmh coloured by chain, top view.
Source organism: Serratia fonticola
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: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179822 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
beta-lactamase Chain: A
Molecule details ›
Chain: A
Length: 270 amino acids
Theoretical weight: 29.42 KDa
Source organism: Serratia fonticola
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6JP75 (Residues: 27-296; Coverage: 95%)
Sequence domains:
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

2 bound ligands:
Ligand EDO 4 x EDO
Ligand MER 1 x MER
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 59.185Å b: 61.955Å c: 79.127Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.117 0.116 0.143
Expression system: Escherichia coli BL21(DE3)

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)