8C5W | pdb_00008c5w

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

PDB DOI: https://doi.org/10.2210/pdb8C5W/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: 2.51 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.231 (Depositor), 0.232 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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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: 75.33 kDa
Atom Count: 4,975
Modeled Residue Count: 634
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HNZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CEF (Subject of Investigation/LOI) Query on CEF 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]	CEFOTAXIME, C3' cleaved, open, bound form C₁₄ H₁₅ N₅ O₅ S₂ NRYMPLKBKFIWQC-YVCCLBOHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.231 (Depositor), 0.232 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.061	α = 90
b = 83.061	β = 90
c = 308.864	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: 2024-11-13
Changes: Database references, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.