7LR9

Crystal structure of KPC-2 S70G/T215P mutant with hydrolyzed imipenem

• PDB DOI: https://doi.org/10.2210/pdb7LR9/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-02-16 Released: 2022-08-10 
• Deposition Author(s): Furey, I., Palzkill, T., Hu, L., Prasad, B.V.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.181 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Crystal structure of KPC-2 T215P mutant

Furey, I.M., Palzkill, T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.26 kDa 
• Atom Count: 4,577 
• Modelled Residue Count: 528 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A, B	268	Klebsiella pneumoniae	Mutation(s): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8YF (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid C12 H19 N3 O5 S KSLAOLVLEKIZMQ-ZXFLCMHBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.181 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.673	α = 91.543
b = 37.743	β = 90.372
c = 82.706	γ = 93.844

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Furey, I., Palzkill, T., Hu, L., Prasad, B.V.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI32956

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary