6Y6U | pdb_00006y6u

Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with Compound 6

• PDB DOI: https://doi.org/10.2210/pdb6Y6U/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-27 Released: 2020-06-24 
• Deposition Author(s): Newman, H., Bellini, D., Dowson, C.G.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.229 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion

Kidd, S.L., Fowler, E., Reinhardt, T., Compton, T., Mateu, N., Newman, H., Bellini, D., Talon, R., McLoughlin, J., Krojer, T., Aimon, A., Bradley, A., Fairhead, M., Brear, P., Diaz-Saez, L., McAuley, K., Sore, H.F., Madin, A., O'Donovan, D.H., Huber, K.V.M., Hyvonen, M., Dowson, C.G., Spring, D.R.

(2020) Chem Sci 11: 10792-10801

• DOI: https://doi.org/10.1039/D0SC01232G

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: 57.16 kDa 
• Atom Count: 4,233 
• Modeled Residue Count: 493 
• Deposited Residue Count: 521 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A	521	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: ftsI, pbpB, PA4418 EC: 3.4.16.4
UniProt
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XD46  Go to UniProtKB:  G3XD46

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ODZ (Subject of Investigation/LOI)	E [auth A]	2-(4-hydroxyphenyl)-~{N}-[(2~{S})-2-methyl-4-oxidanyl-1-oxidanylidene-pent-4-en-2-yl]ethanamide C14 H17 N O4 RSUSHGHDXWZFTH-AWEZNQCLSA-N
GOL	B [auth A], C [auth A], D [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.229 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.568	α = 90
b = 83.128	β = 90
c = 90.063	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
STARANISO	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Newman, H., Bellini, D., Dowson, C.G.

---

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary