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Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin

X-ray diffraction
1.6Å resolution
PDB entry 2ex6 coloured by chain, front view.
PDB entry 2ex6 coloured by chain, side view.
PDB entry 2ex6 coloured by chain, top view.
Source organism: Escherichia coli
Assemblies composition:
monomeric (preferred)
homo dimer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: D-alanyl-D-alanine carboxypeptidase DacB
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Multimeric state: monomeric
Accessible surface area: 20149.55 Å2
Buried surface area: 256.97 Å2
Dissociation area: 128.48 Å2
Dissociation energy (ΔGdiss): 1.58 kcal/mol
Dissociation entropy (TΔSdiss): 0.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-150177
Assembly 2
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Assembly Name: D-alanyl-D-alanine carboxypeptidase DacB
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Multimeric state: homo dimer
Accessible surface area: 36012.38 Å2
Buried surface area: 4790.47 Å2
Dissociation area: 2,138.69 Å2
Dissociation energy (ΔGdiss): 13.06 kcal/mol
Dissociation entropy (TΔSdiss): 14.94 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-150178

Macromolecules

D-alanyl-D-alanine carboxypeptidase DacB
Chain: A
Length: 458 amino acids
Theoretical weight: 49.8 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P24228 (Residues: 21-477; Coverage: 100%)
Gene names: JW3149, b3182, dacB
Pfam: D-Ala-D-Ala carboxypeptidase 3 (S13) family
InterPro:
CATH:
SCOP: Dac-like
D-alanyl-D-alanine carboxypeptidase DacB in PDB entry 2ex6, assembly 1, front view.
D-alanyl-D-alanine carboxypeptidase DacB in PDB entry 2ex6, assembly 1, side view.
D-alanyl-D-alanine carboxypeptidase DacB in PDB entry 2ex6, assembly 1, top view.
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