4WEL | pdb_00004wel

Crystal structure of Pseudomonas aeruginosa PBP3 with SMC-3176

• PDB DOI: https://doi.org/10.2210/pdb4WEL/pdb

• Classification: Penicillin-binding protein/inhibitor
• Organism(s): Pseudomonas aeruginosa PA14
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-10 Released: 2015-04-22 
• Deposition Author(s): Ferguson, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

SAR and Structural Analysis of Siderophore-Conjugated Monocarbam Inhibitors of Pseudomonas aeruginosa PBP3.

Murphy-Benenato, K.E., Dangel, B., Davis, H.E., Durand-Reville, T.F., Ferguson, A.D., Gao, N., Jahic, H., Mueller, J.P., Manyak, E.L., Quiroga, O., Rooney, M., Sha, L., Sylvester, M., Wu, F., Zambrowski, M., Zhao, S.X.

(2015) ACS Med Chem Lett 6: 537-542

• PubMed: 26005529 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00026
• Primary Citation Related Structures: 
  4WEJ, 4WEK, 4WEL


• PubMed Abstract: 
  

  A main challenge in the development of new agents for the treatment of Pseudomonas aeruginosa infections is the identification of chemotypes that efficiently penetrate the cell envelope and are not susceptible to established resistance mechanisms. Siderophore-conjugated monocarbams are attractive because of their ability to hijack the bacteria's iron uptake machinery for transport into the periplasm and their inherent stability to metallo-β-lactamases. Through development of the SAR we identified a number of modifications to the scaffold that afforded active anti-P. aeruginosa agents with good physicochemical properties. Through crystallographic efforts we gained a better understanding into how these compounds bind to the target penicillin binding protein PBP3 and factors to consider for future design.

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Organizational Affiliation: 
• Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.
Structure and Biophysics, and Reagents & Assay Development, Discovery Sciences, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.11 kDa 
• Atom Count: 4,087 
• Modeled Residue Count: 500 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A	538	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: CIA_00399
UniProt
Find proteins for A0A0M3KKZ3 (Pseudomonas aeruginosa PA14) Explore A0A0M3KKZ3  Go to UniProtKB:  A0A0M3KKZ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3LE	B [auth A]	(3S,4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-4-formyl-1-[({3-(5-hydroxy-4-oxo-3,4-dihydropyridin-2-yl)-4-[3-(methylsulfonyl)propyl]-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl}sulfonyl)amino]-3,10,10-trimethyl-1,6-dioxo-9-oxa-2,5,8-triazaundec-7-en-11-oic acid C25 H32 N10 O13 S3 KOZNTWBICKFGGR-BECCELLYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.442	α = 90
b = 83.337	β = 90
c = 89.411	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
MOLREP	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Ferguson, A.D.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2024-11-13
  Changes: Structure summary