9VXS | pdb_00009vxs

Crystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase

PDB DOI: https://doi.org/10.2210/pdb9VXS/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-20 Released: 2025-08-06
Deposition Author(s): Dhankhar, K., Hazra, S.
Funding Organization(s): Indian Council of Medical Research, Board of Research in Nuclear Sciences (BRNS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.268 (Depositor), 0.268 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase

Dhankhar, K., Hazra, S.

To be published.

Macromolecule Content

Total Structure Weight: 59.32 kDa
Atom Count: 4,268
Modeled Residue Count: 534
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase SME-1	A [auth B], B [auth A]	267	Serratia marcescens	Mutation(s): 0 Gene Names: SME-1, blaSME-1, blaSME-4, blaSME1, bpl-1, bplA, sme-2, smeA EC: 3.5.2.6
UniProt
Find proteins for P52682 (Serratia marcescens) Explore P52682 Go to UniProtKB: P52682
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52682
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1II0 (Subject of Investigation/LOI) Query on A1II0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth B]	C [auth B], E [auth A]	3-fluoranyl-7-oxidanyl-8-oxa-7$l^{4}-borabicyclo[4.3.0]nona-1(9),2,4,6-tetraene C₇ H₅ B F O₂ KANFGNKXXLVVNP-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]