› 2z2m

X-ray diffraction
2.6Å resolution

Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae

Released:
DOI: 10.2210/pdb2z2m/pdb
PDB entry 2z2m coloured by chain, front view.
PDB entry 2z2m coloured by chain, side view.
PDB entry 2z2m coloured by chain, top view.
Source organism: Streptococcus pneumoniae
Primary publication:
Crystal structure of cefditoren complexed with Streptococcus pneumoniae penicillin-binding protein 2X: structural basis for its high antimicrobial activity.
Yamada M, Watanabe T, Miyara T, Baba N, Saito J, Takeuchi Y, Ohsawa F
Antimicrob Agents Chemother 51 3902-7 (2007)
PMID: 17724158

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147021 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Penicillin-binding protein 2x Chains: A, D
Molecule details ›
Chains: A, D
Length: 168 amino acids
Theoretical weight: 18.47 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P14677 (Residues: 71-238; Coverage: 22%)
Gene names: SP_0336, pbpX
Sequence domains: Penicillin-binding Protein dimerisation domain
Structure domains:
Penicillin-binding protein 2x Chains: B, E
Molecule details ›
Chains: B, E
Length: 385 amino acids
Theoretical weight: 42 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P14677 (Residues: 241-625; Coverage: 51%)
Gene names: SP_0336, pbpX
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains: DD-peptidase/beta-lactamase superfamily
Penicillin-binding protein 2x Chains: C, F
Molecule details ›
Chains: C, F
Length: 125 amino acids
Theoretical weight: 13.71 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P14677 (Residues: 626-750; Coverage: 17%)
Gene names: SP_0336, pbpX
Sequence domains: PASTA domain

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand CDS 2 x CDS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: P21212
Unit cell:
a: 107.735Å b: 171.205Å c: 89.15Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.221 0.267
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Acylating drugs: redesigning natural covalent inhibitors.
Kluge et al. (2010)
3 more

3 mentions without citation

Crystal structure of cefditoren complexed with Streptococcus pneumoniae penicillin-binding protein 2X: structural basis for its high antimicrobial activity.
Yamada et al. (2007)
2 more