7PSE | pdb_00007pse

Acetyllysine73-incorporated OXA-48 complexed with oxacillin

PDB DOI: https://doi.org/10.2210/pdb7PSE/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-23 Released: 2022-10-05
Deposition Author(s): Zhou, Q., He, Y., Jin, Y.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.289 (Depositor), 0.290 (DCC)
R-Value Work:
0.235 (Depositor), 0.236 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.4 of the entry. See complete history.

Literature

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity

Zhou, Q., Catalan, P., Bell, H., Baumann, P., Cooke, R., Evans, R., Yang, J., Zhang, Z., Zappala, D., Zhang, Y., Blackburn, G.M., He, Y., Jin, Y.

(2023) ACS Cent Sci

DOI: https://doi.org/10.1021/acscentsci.3c00609

Macromolecule Content

Total Structure Weight: 61.64 kDa
Atom Count: 4,099
Modeled Residue Count: 483
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth AAA], B [auth BBB]	260	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: blaOXA EC: 3.5.2.6
UniProt
Find proteins for A0A482LRD5 (Klebsiella pneumoniae) Explore A0A482LRD5 Go to UniProtKB: A0A482LRD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A482LRD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1S6 (Subject of Investigation/LOI) Query on 1S6 Download:Ideal Coordinates CCD File SDF format, chain G [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain G [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain G [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], G [auth BBB]	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid C₁₉ H₂₁ N₃ O₅ S QXXMSXCGXIRLPM-ISTRZQFTSA-N		Interactions Focus chain C [auth AAA] Focus chain G [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain G [auth BBB]
1BO Query on 1BO Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain H [auth BBB] SDF format, chain I [auth BBB] SDF format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain H [auth BBB] MOL2 format, chain I [auth BBB] MOL2 format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain H [auth BBB] mmCIF format, chain I [auth BBB] mmCIF format, chain D [auth AAA]	D [auth AAA], E [auth AAA], H [auth BBB], I [auth BBB]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.289 (Depositor), 0.290 (DCC)
R-Value Work: 0.235 (Depositor), 0.236 (DCC)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.83	α = 90
b = 105.48	β = 90
c = 124.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SADABS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-05

Deposition Author(s):

Zhou, Q.

He, Y.

Jin, Y.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31400663

Revision History (Full details and data files)

Version 1.0: 2022-10-05
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Refinement description
Version 2.1: 2024-01-31
Changes: Refinement description
Version 2.2: 2024-03-06
Changes: Database references
Version 2.3: 2024-10-16
Changes: Structure summary
Version 2.4: 2025-08-06
Changes: Structure summary