1LL5

X-ray crystal structure of AmpC WT beta-lactamase in complex with covalently bound imipenem

• PDB DOI: https://doi.org/10.2210/pdb1LL5/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-26 Released: 2002-11-27 
• Deposition Author(s): Beadle, B.M., Shoichet, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 

Starting Model: experimental

Literature

Structural Basis for Imipenem Inhibition of Class C beta-lactamases

Beadle, B.M., Shoichet, B.K.

(2002) Antimicrob Agents Chemother 46: 3978-3980

• PubMed: 12435704 
• DOI: https://doi.org/10.1128/AAC.46.12.3978-3980.2002
• Primary Citation of Related Structures:  
  1LL5


• PubMed Abstract: 
  

  To determine how imipenem inhibits the class C beta-lactamase AmpC, the X-ray crystal structure of the acyl-enzyme complex was determined to a resolution of 1.80 A. In the complex, the lactam carbonyl oxygen of imipenem has flipped by approximately 180 degrees compared to its expected position; the electrophilic acyl center is thus displaced from the point of hydrolytic attack. This conformation resembles that of imipenem bound to the class A enzyme TEM-1 but is different from that of moxalactam bound to AmpC.

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Organizational Affiliation: 

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611-3008, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.78 kDa 
• Atom Count: 5,816 
• Modelled Residue Count: 709 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	358	Escherichia coli	Mutation(s): 0  Gene Names: K12 EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2	C [auth A], D [auth B]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.457	α = 90
b = 76.911	β = 116.16
c = 98.009	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-27 
Deposition Author(s): Beadle, B.M., Shoichet, B.K.

Revision History  

• Version 1.0: 2002-11-27
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-08-31
  Changes: Other
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary