7Q14

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Imipenem

PDB DOI: https://doi.org/10.2210/pdb7Q14/pdb

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

Deposited: 2021-10-18 Released: 2022-11-16
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: 2.15 Å
R-Value Free: 0.250
R-Value Work: 0.210

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 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: 246.28 kDa
Atom Count: 16,602
Modelled Residue Count: 1,925
Deposited Residue Count: 2,080
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 [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH]	260	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: blaOXA EC: 3.5.2.6
UniProt
Find proteins for A0A482LRD5 (Klebsiella pneumoniae) Explore A0A482LRD5 Go to UniProtKB: A0A482LRD5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A482LRD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ID1 (Subject of Investigation/LOI) Query on ID1 Download Ideal Coordinates CCD File SDF format, chain AA [auth EEE] SDF format, chain DA [auth FFF] SDF format, chain FA [auth GGG] SDF format, chain I [auth AAA] SDF format, chain JA [auth HHH] SDF format, chain N [auth BBB] SDF format, chain U [auth CCC] SDF format, chain Y [auth DDD] MOL2 format, chain AA [auth EEE] MOL2 format, chain DA [auth FFF] MOL2 format, chain FA [auth GGG] MOL2 format, chain I [auth AAA] MOL2 format, chain JA [auth HHH] MOL2 format, chain N [auth BBB] MOL2 format, chain U [auth CCC] MOL2 format, chain Y [auth DDD] mmCIF format, chain AA [auth EEE] mmCIF format, chain DA [auth FFF] mmCIF format, chain FA [auth GGG] mmCIF format, chain I [auth AAA] mmCIF format, chain JA [auth HHH] mmCIF format, chain N [auth BBB] mmCIF format, chain U [auth CCC] mmCIF format, chain Y [auth DDD]	AA [auth EEE] DA [auth FFF] FA [auth GGG] I [auth AAA] JA [auth HHH] AA [auth EEE], DA [auth FFF], FA [auth GGG], I [auth AAA], JA [auth HHH], N [auth BBB], U [auth CCC], Y [auth DDD]	Imipenem C₁₂ H₁₉ N₃ O₄ S NIJGFQHESQFJAG-ZYUZMQFOSA-N		Interactions Focus chain AA [auth EEE] Focus chain DA [auth FFF] Focus chain FA [auth GGG] Focus chain I [auth AAA] Focus chain JA [auth HHH] Focus chain N [auth BBB] Focus chain U [auth CCC] Focus chain Y [auth DDD] Interactions & Density Focus chain AA [auth EEE] Focus chain DA [auth FFF] Focus chain FA [auth GGG] Focus chain I [auth AAA] Focus chain JA [auth HHH] Focus chain N [auth BBB] Focus chain U [auth CCC] Focus chain Y [auth DDD]
BR (Subject of Investigation/LOI) Query on BR Download Ideal Coordinates CCD File SDF format, chain CA [auth EEE] SDF format, chain IA [auth GGG] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain MA [auth HHH] SDF format, chain NA [auth HHH] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain W [auth CCC] SDF format, chain X [auth CCC] SDF format, chain Z [auth DDD] MOL2 format, chain CA [auth EEE] MOL2 format, chain IA [auth GGG] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth HHH] MOL2 format, chain NA [auth HHH] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain W [auth CCC] MOL2 format, chain X [auth CCC] MOL2 format, chain Z [auth DDD] mmCIF format, chain CA [auth EEE] mmCIF format, chain IA [auth GGG] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth HHH] mmCIF format, chain NA [auth HHH] mmCIF format, chain R [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain W [auth CCC] mmCIF format, chain X [auth CCC] mmCIF format, chain Z [auth DDD]	CA [auth EEE] IA [auth GGG] L [auth AAA] M [auth AAA] MA [auth HHH] CA [auth EEE], IA [auth GGG], L [auth AAA], M [auth AAA], MA [auth HHH], NA [auth HHH], R [auth BBB], S [auth BBB], T [auth BBB], W [auth CCC], X [auth CCC], Z [auth DDD]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain CA [auth EEE] Focus chain IA [auth GGG] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth HHH] Focus chain NA [auth HHH] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain CA [auth EEE] Focus chain IA [auth GGG] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth HHH] Focus chain NA [auth HHH] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC] Focus chain Z [auth DDD]
1BO Query on 1BO Download Ideal Coordinates CCD File SDF format, chain BA [auth EEE] SDF format, chain EA [auth FFF] SDF format, chain GA [auth GGG] SDF format, chain HA [auth GGG] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain KA [auth HHH] SDF format, chain LA [auth HHH] SDF format, chain O [auth BBB] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain V [auth CCC] MOL2 format, chain BA [auth EEE] MOL2 format, chain EA [auth FFF] MOL2 format, chain GA [auth GGG] MOL2 format, chain HA [auth GGG] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth HHH] MOL2 format, chain LA [auth HHH] MOL2 format, chain O [auth BBB] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain V [auth CCC] mmCIF format, chain BA [auth EEE] mmCIF format, chain EA [auth FFF] mmCIF format, chain GA [auth GGG] mmCIF format, chain HA [auth GGG] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain KA [auth HHH] mmCIF format, chain LA [auth HHH] mmCIF format, chain O [auth BBB] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain V [auth CCC]	BA [auth EEE] EA [auth FFF] GA [auth GGG] HA [auth GGG] J [auth AAA] BA [auth EEE], EA [auth FFF], GA [auth GGG], HA [auth GGG], J [auth AAA], K [auth AAA], KA [auth HHH], LA [auth HHH], O [auth BBB], P [auth BBB], Q [auth BBB], V [auth CCC]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain BA [auth EEE] Focus chain EA [auth FFF] Focus chain GA [auth GGG] Focus chain HA [auth GGG] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain KA [auth HHH] Focus chain LA [auth HHH] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain V [auth CCC] Interactions & Density Focus chain BA [auth EEE] Focus chain EA [auth FFF] Focus chain GA [auth GGG] Focus chain HA [auth GGG] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain KA [auth HHH] Focus chain LA [auth HHH] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain V [auth CCC]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.250
R-Value Work: 0.210
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.398	α = 90
b = 161.934	β = 90.513
c = 107.782	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Zhou, Q.

He, Y.

Jin, Y.

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

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Refinement description
Version 2.1: 2024-01-31
Changes: Refinement description
Version 2.2: 2024-03-06
Changes: Database references
Version 2.3: 2024-10-23
Changes: Structure summary