8C5O

Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis in complex with Vaborbactam

PDB DOI: https://doi.org/10.2210/pdb8C5O/pdb

Classification: PENICILLIN-BINDING PROTEIN
Organism(s): Staphylococcus epidermidis RP62A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-10 Released: 2023-12-13
Deposition Author(s): Schwinzer, M., Brognaro, H., Rohde, H., Betzel, C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.227
R-Value Work: 0.199
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure and Dynamics of the Penicillin-Binding Protein 3 from Staphylococcus Epidermidis Native and in Complex with Cefotaxime and Vaborbactam

Schwinzer, M., Brognaro, H., Rohde, H., Betzel, C.

(2023) Int J Appl Biol Pharm

DOI: https://doi.org/10.26502/ijabpt.202127

Macromolecule Content

Total Structure Weight: 75.23 kDa
Atom Count: 5,228
Modelled Residue Count: 632
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A	668	Staphylococcus epidermidis RP62A	Mutation(s): 0 Gene Names: pbp3, SERP1117
UniProt
Find proteins for Q5HNZ7 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)) Explore Q5HNZ7 Go to UniProtKB: Q5HNZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5HNZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4D6 (Subject of Investigation/LOI) Query on 4D6 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Vaborbactam C₁₂ H₁₆ B N O₅ S IOOWNWLVCOUUEX-WPRPVWTQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.227
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.152	α = 90
b = 83.152	β = 90
c = 306.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-11-06
Changes: Database references, 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.