6ZRP | pdb_00006zrp

Crystal structure of class D Beta-lactamase OXA-48 in complex with meropenem

PDB DOI: https://doi.org/10.2210/pdb6ZRP/pdb

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

Deposited: 2020-07-14 Released: 2021-07-21
Deposition Author(s): Tassone, G., De Luca, F., Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S., Doquier, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.187 (Depositor), 0.187 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanistic insights into carbapenem hydrolysis by OXA-48 and the OXA10-derived hybrids OXA-10 loop24 and loop48

Tassone, G., De Luca, F., Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S., Doquier, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 124.43 kDa
Atom Count: 9,498
Modeled Residue Count: 970
Deposited Residue Count: 1,060
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, D	265	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, blaOXA-48, KPE71T_00045 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0 Go to UniProtKB: Q6XEC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	B, C	265	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768... bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0 Go to UniProtKB: Q6XEC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 E [auth A] SDF format, chain J [auth B] SDF format, chain V [auth D] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain V [auth D] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain V [auth D] mmCIF format, chain P [auth C]	E [auth A], J [auth B], P [auth C], V [auth D]	(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 E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth D] SDF format, chain Y [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D]	AA [auth D] BA [auth D] F [auth A] G [auth A] H [auth A] AA [auth D], BA [auth D], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.187 (Depositor), 0.187 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.994	α = 90
b = 125.286	β = 77.7
c = 105.199	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2022-02-02
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description