2ZC4

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from Streptococcus pneumoniae

Yamada, M.Watanabe, T.Baba, N.Takeuchi, Y.Ohsawa, F.Gomi, S.

(2008) Antimicrob Agents Chemother 52: 2053-2060

  • DOI: https://doi.org/10.1128/AAC.01456-07
  • Primary Citation of Related Structures:  
    2ZC3, 2ZC4, 2ZC5, 2ZC6

  • PubMed Abstract: 

    Biapenem is a parenteral carbapenem antibiotic that exhibits wide-ranging antibacterial activity, remarkable chemical stability, and extensive stability against human renal dehydropeptidase-I. Tebipenem is the active form of tebipenem pivoxil, a novel oral carbapenem antibiotic that has a high level of bioavailability in humans, in addition to the above-mentioned features. beta-lactam antibiotics, including carbapenems, target penicillin-binding proteins (PBPs), which are membrane-associated enzymes that play essential roles in peptidoglycan biosynthesis. To envisage the binding of carbapenems to PBPs, we determined the crystal structures of the trypsin-digested forms of both PBP 2X and PBP 1A from Streptococcus pneumoniae strain R6, each complexed with biapenem or tebipenem. The structures of the complexes revealed that the carbapenem C-2 side chains form hydrophobic interactions with Trp374 and Thr526 of PBP 2X and with Trp411 and Thr543 of PBP 1A. The Trp and Thr residues are conserved in PBP 2B. These results suggest that interactions between the C-2 side chains of carbapenems and the conserved Trp and Thr residues in PBPs play important roles in the binding of carbapenems to PBPs.


  • Organizational Affiliation

    Pharmaceutical Research Center, Meiji Seika Kaisha, Ltd., 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567, Japan. mototsugu_yamada@meiji.co.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2X
A, D
168Streptococcus pneumoniaeMutation(s): 0 
Gene Names: pbpX
UniProt
Find proteins for P14677 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P14677 
Go to UniProtKB:  P14677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14677
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2X
B, E
385Streptococcus pneumoniaeMutation(s): 0 
Gene Names: pbpX
UniProt
Find proteins for P14677 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P14677 
Go to UniProtKB:  P14677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14677
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2X
C, F
125Streptococcus pneumoniaeMutation(s): 0 
Gene Names: pbpX
UniProt
Find proteins for P14677 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P14677 
Go to UniProtKB:  P14677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14677
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEB
Query on TEB

Download Ideal Coordinates CCD File 
G [auth B],
I [auth E]
(4R,5S)-3-(1-(4,5-dihydrothiazol-2-yl)azetidin-3-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4-methyl-4,5- dihydro-1H-pyrrole-2-carboxylic acid
C16 H23 N3 O4 S2
PGCJBZBFZXWIGF-CNVPUSNMSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.305α = 90
b = 172.063β = 90
c = 88.805γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description