7O5N

Crystal Structure of a Class D carbapenemase complexed with Avibactam

PDB DOI: https://doi.org/10.2210/pdb7O5N/pdb

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

Deposited: 2021-04-09 Released: 2022-04-20
Deposition Author(s): Zhou, Q., Zhang, Z., He, Y., Jin, Y.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216
R-Value Work: 0.188

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

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: 122.84 kDa
Atom Count: 8,862
Modelled Residue Count: 969
Deposited Residue Count: 1,040
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 [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NXL (Subject of Investigation/LOI) Query on NXL Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain N [auth BBB] SDF format, chain R [auth CCC] SDF format, chain W [auth DDD] MOL2 format, chain G [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain R [auth CCC] MOL2 format, chain W [auth DDD] mmCIF format, chain G [auth AAA] mmCIF format, chain N [auth BBB] mmCIF format, chain R [auth CCC] mmCIF format, chain W [auth DDD]	G [auth AAA], N [auth BBB], R [auth CCC], W [auth DDD]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C₇ H₁₃ N₃ O₆ S WJDGWXPPFHLLNL-RITPCOANSA-N		Interactions Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain R [auth CCC] Focus chain W [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain R [auth CCC] Focus chain W [auth DDD]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth BBB] SDF format, chain P [auth CCC] SDF format, chain V [auth DDD] MOL2 format, chain K [auth BBB] MOL2 format, chain P [auth CCC] MOL2 format, chain V [auth DDD] mmCIF format, chain K [auth BBB] mmCIF format, chain P [auth CCC] mmCIF format, chain V [auth DDD]	K [auth BBB], P [auth CCC], V [auth DDD]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth BBB] Focus chain P [auth CCC] Focus chain V [auth DDD] Interactions & Density Focus chain K [auth BBB] Focus chain P [auth CCC] Focus chain V [auth DDD]
1BO Query on 1BO Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain Q [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain Q [auth CCC] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain Q [auth CCC]	E [auth AAA], F [auth AAA], L [auth BBB], M [auth BBB], Q [auth CCC]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain Q [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain Q [auth CCC]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain O [auth BBB] SDF format, chain S [auth CCC] SDF format, chain T [auth CCC] SDF format, chain U [auth CCC] SDF format, chain X [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain S [auth CCC] MOL2 format, chain T [auth CCC] MOL2 format, chain U [auth CCC] MOL2 format, chain X [auth DDD] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain O [auth BBB] mmCIF format, chain S [auth CCC] mmCIF format, chain T [auth CCC] mmCIF format, chain U [auth CCC] mmCIF format, chain X [auth DDD]	H [auth AAA] I [auth AAA] J [auth AAA] O [auth BBB] S [auth CCC] H [auth AAA], I [auth AAA], J [auth AAA], O [auth BBB], S [auth CCC], T [auth CCC], U [auth CCC], X [auth DDD]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain X [auth DDD] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain X [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216
R-Value Work: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.749	α = 90
b = 107.959	β = 90
c = 125.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

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: 2022-04-20
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-03-06
Changes: Database references
Version 1.3: 2024-11-13
Changes: Structure summary