9JNA | pdb_00009jna

Crystal Structure of SME-1 E166A mutant in complex with Meropenem

PDB DOI: https://doi.org/10.2210/pdb9JNA/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-09-23 Released: 2025-10-01
Deposition Author(s): Dhankhar, K., Hazra, S.
Funding Organization(s): Board of Research in Nuclear Sciences (BRNS), Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (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 SME-1 E166A mutant in complex with Meropenem

Dhankhar, K., Hazra, S.

To be published.

Macromolecule Content

Total Structure Weight: 62.03 kDa
Atom Count: 4,282
Modeled Residue Count: 534
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	275	Serratia marcescens	Mutation(s): 1 Gene Names: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 EC: 3.5.2.6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DWZ (Subject of Investigation/LOI) Query on DWZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C₁₇ H₂₇ N₃ O₅ S UUIYVKJXUXGPKB-VGWSNGFZSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]