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

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AD68
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bicyclic peptide inhibitor	B [auth A]	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
29N (Subject of Investigation/LOI) Query on 29N Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one C₁₂ H₂₁ N₃ O₃ AEPJNZPJFYDQLM-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.