7E63

The crystal structure of peptidoglycan peptidase in complex with inhibitor 2-1

• PDB DOI: https://doi.org/10.2210/pdb7E63/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-02-21 Released: 2022-02-23 
• Deposition Author(s): Choi, Y., Min, K.J., Yoon, H.J., Lee, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 

Literature

Structure-based inhibitor design for reshaping bacterial morphology

Choi, Y., Park, J.S., Kim, J., Min, K., Mahasenan, K., Kim, C., Yoon, H.J., Lim, S., Cheon, D.H., Lee, Y., Ryu, S., Mobashery, S., Kim, B.M., Lee, H.H.

(2022) Commun Biol 5: 395

• DOI: https://doi.org/10.1038/s42003-022-03355-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 57.44 kDa 
• Atom Count: 4,216 
• Modelled Residue Count: 510 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M23	A, B	255	Campylobacter jejuni	Mutation(s): 1  Gene Names: A8118_01115

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HY9 (Subject of Investigation/LOI)	E [auth B]	2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(cyclopentylmethyl)amino]ethanoic acid C17 H30 N4 O6 CZUXSTKXXAXBTE-RISCZKNCSA-N
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.872	α = 90
b = 90.734	β = 90
c = 100.946	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Choi, Y., Min, K.J., Yoon, H.J., Lee, H.H.

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description