7L5T | pdb_00007l5t

Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid

PDB DOI: https://doi.org/10.2210/pdb7L5T/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-22 Released: 2021-12-29
Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.196 (Depositor), 0.206 (DCC)
R-Value Work:
0.167 (Depositor), 0.176 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 57.48 kDa
Atom Count: 4,402
Modeled Residue Count: 493
Deposited Residue Count: 496
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	248	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: OXA-14, blaOXA EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa) Explore P14489 Go to UniProtKB: P14489
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ISS (Subject of Investigation/LOI) Query on ISS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	(2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal C₇ H₁₁ N O₃ WWFGWBHKRFILGQ-HNQUOIGGSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	M [auth A], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain U [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.196 (Depositor), 0.206 (DCC)
R-Value Work: 0.167 (Depositor), 0.176 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data: https://doi.org/10.18430/m37l5t

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.94	α = 90
b = 95.451	β = 90
c = 125.974	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2026-03-11
Changes: Database references, Other, Structure summary