9F0V | pdb_00009f0v

Structure of KPC-2 complexed with benzoxaborole AK-63

• PDB DOI: https://doi.org/10.2210/pdb9F0V/pdb

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


• Deposited: 2024-04-17 Released: 2025-08-06 
• Deposition Author(s): Tooke, C.L., Hinchliffe, P., Spencer, J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.167 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Structure of KPC-2 complexed with benzoxaborole AK-63

Tooke, C.L., Hinchliffe, P., Spencer, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.47 kDa 
• Atom Count: 2,665 
• Modeled Residue Count: 270 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.167 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.15	α = 90
b = 79.08	β = 90
c = 55.85	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Tooke, C.L., Hinchliffe, P., Spencer, J.

---

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/T016035/1

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release