7NRJ

Crystal Structure of a Class D carbapenemase complexed with iodide

PDB DOI: https://doi.org/10.2210/pdb7NRJ/pdb

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

Deposited: 2021-03-04 Released: 2022-03-23
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: 1.67 Å
R-Value Free: 0.197
R-Value Work: 0.166

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 123.93 kDa
Atom Count: 9,013
Modelled Residue Count: 967
Deposited Residue Count: 1,040
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]	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
IOD (Subject of Investigation/LOI) Query on IOD Download Ideal Coordinates CCD File SDF format, chain CA [auth DDD] SDF format, chain DA [auth DDD] SDF format, chain EA [auth DDD] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] 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 P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain X [auth CCC] SDF format, chain Y [auth CCC] SDF format, chain W [auth CCC] MOL2 format, chain CA [auth DDD] MOL2 format, chain DA [auth DDD] MOL2 format, chain EA [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] 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 P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain X [auth CCC] MOL2 format, chain Y [auth CCC] MOL2 format, chain W [auth CCC] mmCIF format, chain CA [auth DDD] mmCIF format, chain DA [auth DDD] mmCIF format, chain EA [auth DDD] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] 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 P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain X [auth CCC] mmCIF format, chain Y [auth CCC] mmCIF format, chain W [auth CCC]	CA [auth DDD] DA [auth DDD] EA [auth DDD] F [auth AAA] G [auth AAA] CA [auth DDD], DA [auth DDD], EA [auth DDD], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], O [auth BBB], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB], W [auth CCC], X [auth CCC], Y [auth CCC]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain EA [auth DDD] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC] Focus chain Y [auth CCC] Interactions & Density Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain EA [auth DDD] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC] Focus chain Y [auth CCC]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth DDD] SDF format, chain M [auth BBB] SDF format, chain V [auth CCC] SDF format, chain L [auth BBB] MOL2 format, chain AA [auth DDD] MOL2 format, chain M [auth BBB] MOL2 format, chain V [auth CCC] MOL2 format, chain L [auth BBB] mmCIF format, chain AA [auth DDD] mmCIF format, chain M [auth BBB] mmCIF format, chain V [auth CCC] mmCIF format, chain L [auth BBB]	AA [auth DDD], L [auth BBB], M [auth BBB], V [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth DDD] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain V [auth CCC] Interactions & Density Focus chain AA [auth DDD] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain V [auth CCC]
1BO Query on 1BO Download Ideal Coordinates CCD File SDF format, chain BA [auth DDD] SDF format, chain E [auth AAA] SDF format, chain K [auth BBB] SDF format, chain N [auth BBB] SDF format, chain T [auth CCC] SDF format, chain U [auth CCC] SDF format, chain Z [auth DDD] MOL2 format, chain BA [auth DDD] MOL2 format, chain E [auth AAA] MOL2 format, chain K [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain T [auth CCC] MOL2 format, chain U [auth CCC] MOL2 format, chain Z [auth DDD] mmCIF format, chain BA [auth DDD] mmCIF format, chain E [auth AAA] mmCIF format, chain K [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain T [auth CCC] mmCIF format, chain U [auth CCC] mmCIF format, chain Z [auth DDD]	BA [auth DDD] E [auth AAA] K [auth BBB] N [auth BBB] T [auth CCC] BA [auth DDD], E [auth AAA], K [auth BBB], N [auth BBB], T [auth CCC], U [auth CCC], Z [auth DDD]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain BA [auth DDD] Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain N [auth BBB] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain BA [auth DDD] Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain N [auth BBB] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain Z [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: 1.67 Å
R-Value Free: 0.197
R-Value Work: 0.166
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.764	α = 90
b = 126.86	β = 98.354
c = 111.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-23

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: 2022-03-23
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