9Z5T | pdb_00009z5t

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079

• PDB DOI: https://doi.org/10.2210/pdb9Z5T/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-11-12 Released: 2026-02-04 
• Deposition Author(s): Bala, S., Stratton, C.M., Davies, C.
• 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: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae

Uehara, T., Zulli, A.L., Miller, B., Avery, L.M., Boyd, S.A., Chatwin, C.L., Chu, G.H., Drager, A., Edwards, M., Hart, S.E., Myers, C.L., Rongola, G., Stevenson, A., Uehara, K., Yi, F., Wang, B., Liu, Z., Wang, M., Zhao, Z., Zhao, X., Zhao, H., Stratton, C.M., Bala, S., Davies, C., Travc, R., Jerse, A.E., Pevear, D.C., Burns, C.J., Daigle, D.M., Condon, S.M.

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)

Macromolecule Content 

• Total Structure Weight: 36.01 kDa 
• Atom Count: 2,562 
• Modeled Residue Count: 321 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peptidoglycan D,D-transpeptidase PenA	A	330	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for F2Z7K9 (Neisseria gonorrhoeae) Explore F2Z7K9  Go to UniProtKB:  F2Z7K9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1C02 (Subject of Investigation/LOI)	B [auth A]	(3R)-7-fluoro-3-{[(2R)-2-(3-fluoro-4-phosphonophenyl)-2-{[3-(methanesulfonyl)-2-oxoimidazolidine-1-carbonyl]amino}acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid C22 H22 B F2 N4 O12 P S GGGMICNUPVVXMH-DOTOQJQBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.865	α = 90
b = 60.151	β = 90
c = 111.023	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Bala, S., Stratton, C.M., Davies, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI141239
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI164794

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release