5UL8 | pdb_00005ul8

Apo KPC-2 beta-lactamase crystal structure at 1.15 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5UL8/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-24 Released: 2017-04-26 
• Deposition Author(s): Pemberton, O.A., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.139 (Depositor), 0.122 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.121 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Literature

Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2).

Pemberton, O.A., Zhang, X., Chen, Y.

(2017) J Med Chem 60: 3525-3530

• PubMed: 28388065 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00158
• Primary Citation Related Structures: 
  5UJ3, 5UJ4, 5UL8


• PubMed Abstract: 
  

  Carbapenem-resistant Enterobacteriaceae are resistant to most β-lactam antibiotics due to the production of the Klebsiella pneumoniae carbapenemase (KPC-2) class A β-lactamase. Here, we present the first product complex crystal structures of KPC-2 with β-lactam antibiotics containing hydrolyzed cefotaxime and faropenem. They provide experimental insights into substrate recognition by KPC-2 and its unique cephalosporinase/carbapenemase activity. These structures also represent the first product complexes for a wild-type serine β-lactamase, elucidating the product release mechanism of these enzymes in general.

---

Organizational Affiliation: 
• Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.28 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 271 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A	290	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, kpc, kpc1 EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae) Explore Q9F663  Go to UniProtKB:  Q9F663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.139 (Depositor), 0.122 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.121 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.8	α = 90
b = 60.2	β = 90
c = 78.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOSFLM	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Pemberton, O.A., Chen, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI103158-04

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary