7PEH | pdb_00007peh

Apo OXA-48 with fully carbamylated Lys73 at pH 7.5

PDB DOI: https://doi.org/10.2210/pdb7PEH/pdb

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

Deposited: 2021-08-10 Released: 2022-08-24
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: 1.92 Å
R-Value Free:
0.249 (Depositor), 0.248 (DCC)
R-Value Work:
0.218 (Depositor), 0.216 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PEH

This is version 1.3 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: 121.54 kDa
Atom Count: 8,445
Modeled Residue Count: 968
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	260	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1BO Query on 1BO Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain I [auth BBB] SDF format, chain J [auth CCC] SDF format, chain K [auth DDD] SDF format, chain H [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth CCC] MOL2 format, chain K [auth DDD] MOL2 format, chain H [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth CCC] mmCIF format, chain K [auth DDD] mmCIF format, chain H [auth BBB]	E [auth AAA] F [auth AAA] G [auth AAA] H [auth BBB] I [auth BBB] E [auth AAA], F [auth AAA], G [auth AAA], H [auth BBB], I [auth BBB], J [auth CCC], K [auth DDD]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth CCC] Focus chain K [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth CCC] Focus chain K [auth DDD]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.249 (Depositor), 0.248 (DCC)
R-Value Work: 0.218 (Depositor), 0.216 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.003	α = 90
b = 106.976	β = 90
c = 124.611	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-03-06
Changes: Database references
Version 1.3: 2025-08-06
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.