› 2y2h

X-ray diffraction
1.96Å resolution

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA2)

Released:
DOI: 10.2210/pdb2y2h/pdb
PDB entry 2y2h coloured by chain, front view.
PDB entry 2y2h coloured by chain, side view.
PDB entry 2y2h coloured by chain, top view.
Source organism: Streptococcus pneumoniae R6
Primary publication:
Structure-guided design of cell wall biosynthesis inhibitors that overcome β-lactam resistance in Staphylococcus aureus (MRSA).
Contreras-Martel C, Amoroso A, Woon EC, Zervosen A, Inglis S, Martins A, Verlaine O, Rydzik AM, Job V, Luxen A, Joris B, Schofield CJ, Dessen A
ACS Chem Biol 6 943-51 (2011)
PMID: 21732689

Function and Biology Details

Reaction catalysed: 
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181431 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
peptidoglycan glycosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 494 amino acids
Theoretical weight: 54.1 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7CRA4 (Residues: 321-791; Coverage: 57%)
Gene names: pbp1b, spr1909
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZA2 2 x ZA2
Ligand SO4 2 x SO4
Ligand CL 18 x CL
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 95.992Å b: 100.484Å c: 143.969Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.212 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

Resistance to antibiotics targeted to the bacterial cell wall.
Nikolaidis et al. (2014)
13 more

1 mention without citation

Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one.
Deghady et al. (2021)