4NQ5 | pdb_00004nq5

Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 complexed with compound CS319

PDB DOI: https://doi.org/10.2210/pdb4NQ5/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Bacillus cereus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-23 Released: 2014-11-26
Deposition Author(s): Gonzalez, J.M., Gonzalez, M.M., Vila, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.254 (Depositor), 0.260 (DCC)
R-Value Work:
0.192 (Depositor), 0.202 (DCC)
R-Value Observed:
0.199 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Inhibition of metallo-lactamases with bicyclic compounds

Gonzalez, M.M., Gonzalez, J.M., Vila, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 24.83 kDa
Atom Count: 1,671
Modeled Residue Count: 216
Deposited Residue Count: 222
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase 2	A	222	Bacillus cereus	Mutation(s): 0 Gene Names: blm EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus) Explore P04190 Go to UniProtKB: P04190
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04190
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3C7 Query on 3C7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid C₇ H₁₁ N O₂ S₃ ZTWVMVSSSBGFHH-JKUQZMGJSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.254 (Depositor), 0.260 (DCC)
R-Value Work: 0.192 (Depositor), 0.202 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.172	α = 90
b = 60.828	β = 93.01
c = 69.41	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.