7DML

OXA-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid

PDB DOI: https://doi.org/10.2210/pdb7DML/pdb

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

Deposited: 2020-12-04 Released: 2021-12-15
Deposition Author(s): Li, G.-B., Yan, Y.-H.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.172 (Depositor), 0.180 (DCC)
R-Value Work:
0.138 (Depositor), 0.150 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Design and enantioselective synthesis of 3-(alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance

Xiao, Y.C., Chen, X.P., Deng, J., Yan, Y.H., Zhu, K.R., Li, G., Yu, J.L., Brem, J., Chen, F., Schofield, C.J., Li, G.B.

(2021) Chem Commun (Camb) 57: 7709-7712

DOI: https://doi.org/10.1039/D1CC03026D

Macromolecule Content

Total Structure Weight: 122.57 kDa
Atom Count: 8,967
Modelled Residue Count: 964
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	265	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, bla_2, bla_3, blaOXA-48 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0 Go to UniProtKB: Q6XEC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H9O (Subject of Investigation/LOI) Query on H9O Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	2-[(3R)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid C₁₀ H₉ B O₄ BRBGRVSFRVLGNY-VIFPVBQESA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.172 (Depositor), 0.180 (DCC)
R-Value Work: 0.138 (Depositor), 0.150 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.455	α = 90
b = 105.865	β = 107.81
c = 94.118	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	81874291
National Science Foundation (NSF, China)	China	82073698

Revision History (Full details and data files)

Version 1.0: 2021-12-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.