4CJN

Crystal structure of PBP2a from MRSA in complex with quinazolinone ligand

• PDB DOI: https://doi.org/10.2210/pdb4CJN/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-21 Released: 2015-02-11 
• Deposition Author(s): Bouley, R., Otero, L.H., Rojas-Altuve, A., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 148.06 kDa 
• Atom Count: 10,669 
• Modelled Residue Count: 1,284 
• Deposited Residue Count: 1,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN BINDING PROTEIN 2 PRIME	A, B	642	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  EC: 3.4.16.4
UniProt
Find proteins for A0A0J9X1X5 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0J9X1X5  Go to UniProtKB:  A0A0J9X1X5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QNZ	L [auth B]	(E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl)benzoic acid C24 H15 N3 O3 XWICYONKRAKFAQ-OUKQBFOZSA-N
MUR	G [auth A], M [auth B]	beta-muramic acid C9 H17 N O7 MSFSPUZXLOGKHJ-KTZFPWNASA-N
CD	C [auth A], D [auth A], H [auth B], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	E [auth A], F [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
QNZ	Binding MOAD:  4CJN	Kd: 1.75e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.05	α = 90
b = 103.773	β = 90
c = 186.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Bouley, R., Otero, L.H., Rojas-Altuve, A., Hermoso, J.A.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary