› 7mdc

X-ray diffraction
2.7Å resolution

Full-length wildtype ClbP inhibited by hexanoyl-D-asparagine boronic acid

Released:
DOI: 10.2210/pdb7mdc/pdb
PDB entry 7mdc coloured by chain, front view.
PDB entry 7mdc coloured by chain, side view.
PDB entry 7mdc coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A small molecule inhibitor prevents gut bacterial genotoxin production.
Volpe MR, Velilla JA, Daniel-Ivad M, Yao JJ, Stornetta A, Villalta PW, Huang HC, Bachovchin DA, Balbo S, Gaudet R, Balskus EP
OpenAccess logo Nat Chem Biol (2022)
PMID: 36253549

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-555465 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase Chain: A
Molecule details ›
Chain: A
Length: 480 amino acids
Theoretical weight: 52.97 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0P7K6 (Residues: 31-504; Coverage: 100%)
Gene names: D3C88_24740, EPS76_05775, EWK56_23765, FPI65_12330, PWL68_000581, clbP
Sequence domains: Beta-lactamase

Ligands and Environments

6 bound ligands:
Ligand 2PE 7 x 2PE
Ligand DMS 1 x DMS
Ligand 97N 1 x 97N
Ligand YX7 1 x YX7
Ligand SO4 1 x SO4
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P42212
Unit cell:
a: 96.718Å b: 96.718Å c: 183.382Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.193 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Bacteria in cancer initiation, promotion and progression.
El Tekle et al. (2023)
4 more

2 mentions without citation

Structure and function of prodrug-activating peptidases.
Velilla et al. (2023)
1 more