9OTG | pdb_00009otg

Crystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae strain FA19 acylated by piperacillin

PDB DOI: https://doi.org/10.2210/pdb9OTG/pdb

Classification: LIGASE
Organism(s): Neisseria gonorrhoeae FA19
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2025-05-27 Released: 2026-06-03
Deposition Author(s): Stratton, C.M., Bala, S., Davies, C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.266 (Depositor), 0.268 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Tyrosine-422 plays a crucial role in acylation and transpeptidation in penicillin-binding protein 2 from Neisseria gonorrhoeae

Stratton, C.M., Bala, S., Bivins, M.M., Nicholas, R.A., Davies, C.

To be published.

Macromolecule Content

Total Structure Weight: 71.69 kDa
Atom Count: 4,930
Modeled Residue Count: 641
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peptidoglycan D,D-transpeptidase PenA	A, B	329	Neisseria gonorrhoeae FA19	Mutation(s): 0 Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for P08149 (Neisseria gonorrhoeae) Explore P08149 Go to UniProtKB: P08149
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JPP (Subject of Investigation/LOI) Query on JPP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	Piperacillin (Open Form) C₂₃ H₂₉ N₅ O₇ S CJYMHKMECTVNSA-XLMAVXFVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.266 (Depositor), 0.268 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.986	α = 90
b = 77.962	β = 90.75
c = 87.237	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.