7PEP

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem

PDB DOI: https://doi.org/10.2210/pdb7PEP/pdb

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

Deposited: 2021-08-11 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: 1.70 Å
R-Value Free: 0.231
R-Value Work: 0.199

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

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: 122.91 kDa
Atom Count: 9,129
Modelled Residue Count: 976
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIW (Subject of Investigation/LOI) Query on HIW Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain G [auth BBB] SDF format, chain M [auth CCC] SDF format, chain O [auth DDD] MOL2 format, chain E [auth AAA] MOL2 format, chain G [auth BBB] MOL2 format, chain M [auth CCC] MOL2 format, chain O [auth DDD] mmCIF format, chain E [auth AAA] mmCIF format, chain G [auth BBB] mmCIF format, chain M [auth CCC] mmCIF format, chain O [auth DDD]	E [auth AAA], G [auth BBB], M [auth CCC], O [auth DDD]	(2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid C₁₂ H₁₉ N₃ O₅ S GGEWNUMDSNUHAH-LURQLKTLSA-N		Interactions Focus chain E [auth AAA] Focus chain G [auth BBB] Focus chain M [auth CCC] Focus chain O [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain G [auth BBB] Focus chain M [auth CCC] Focus chain O [auth DDD]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain H [auth BBB] SDF format, chain I [auth BBB] SDF format, chain J [auth BBB] SDF format, chain N [auth CCC] SDF format, chain P [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain H [auth BBB] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain N [auth CCC] MOL2 format, chain P [auth DDD] mmCIF format, chain F [auth AAA] mmCIF format, chain H [auth BBB] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain N [auth CCC] mmCIF format, chain P [auth DDD]	F [auth AAA] H [auth BBB] I [auth BBB] J [auth BBB] N [auth CCC] F [auth AAA], H [auth BBB], I [auth BBB], J [auth BBB], N [auth CCC], P [auth DDD]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain N [auth CCC] Focus chain P [auth DDD] Interactions & Density Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain N [auth CCC] Focus chain P [auth DDD]
1BO Query on 1BO Download Ideal Coordinates CCD File SDF format, chain K [auth CCC] SDF format, chain L [auth CCC] MOL2 format, chain K [auth CCC] MOL2 format, chain L [auth CCC] mmCIF format, chain K [auth CCC] mmCIF format, chain L [auth CCC]	K [auth CCC], L [auth CCC]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain K [auth CCC] Focus chain L [auth CCC] Interactions & Density Focus chain K [auth CCC] Focus chain L [auth CCC]