8RTZ

The structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8RTZ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-29 Released: 2024-04-03 
• Deposition Author(s): Newman, H., Rowland, C.E., Dods, R., Lewis, N., Stanway, S.J., Bellini, D., Beswick, P.
• Funding Organization(s): Innovate UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 

Literature

Discovery and chemical optimisation of a Potent, Bi-cyclic (Bicycle) Antimicrobial Inhibitor of Escherichia coli PBP3

Rowland, C.E., Newman, H., Martin, T.T., Dods, R., Bournakas, N., Wagstaff, J.M., Lewis, N., Stanway, S.J., Blamforth, M., Kessler, C., van Rietschoten, K., Bellini, D., Roper, D.I., Lloyd, A.J., Dowson, C.G., Skynner, M.J., Beswick, P., Dawson, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 38.88 kDa 
• Atom Count: 2,840 
• Modelled Residue Count: 337 
• Deposited Residue Count: 363 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A [auth AAA]	348	Escherichia coli	Mutation(s): 0  Gene Names: ftsI, pbpB, b0084, JW0082 EC: 3.4.16.4
UniProt
Find proteins for P0AD68 (Escherichia coli (strain K12)) Explore P0AD68  Go to UniProtKB:  P0AD68

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bicyclic peptide inhibitor	B [auth A]	15	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29N (Subject of Investigation/LOI)	C [auth A]	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one C12 H21 N3 O3 AEPJNZPJFYDQLM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.89	α = 90
b = 152.181	β = 90
c = 43.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Newman, H., Rowland, C.E., Dods, R., Lewis, N., Stanway, S.J., Bellini, D., Beswick, P.

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Funding Organization	Location	Grant Number
Innovate UK	United Kingdom	971626Q1
Innovate UK	United Kingdom	77556
Innovate UK	United Kingdom	82975

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release