3B3X

Crystal structure of class A beta-lactamase of Bacillus licheniformis BS3 with aminocitrate

PDB DOI: https://doi.org/10.2210/pdb3B3X/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Bacillus licheniformis
Mutation(s): No

Deposited: 2007-10-23 Released: 2007-11-13
Deposition Author(s): Sauvage, E., Herman, R., Kerff, F., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.288
R-Value Work: 0.220
R-Value Observed: 0.223

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2-Aminopropane-1,2,3-tricarboxylic acid: Synthesis and co-crystallization with the class A beta-lactamase BS3 of Bacillus licheniformis

Beck, J., Sauvage, E., Charlier, P., Marchand-Brynaert, J.

(2008) Bioorg Med Chem Lett 18: 3764-3768

PubMed: 18515103 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.05.045
Primary Citation of Related Structures:
3B3X

PubMed Abstract:
The title compound 4 has been prepared in four steps from ethylglycinate in 63% overall yield. This amino analog of citric acid has been co-crystallized with the class A beta-lactamase BS3 of Bacillus licheniformis and the structure of the complex fully analyzed by X-ray diffraction. Tris-ethyl aminocitrate 3 and the free tris-acid 4 have been tested against a member beta-lactamase from all distinct subgroups. They are novel inhibitors of class A beta-lactamases, still modest but more potent than citrate and isocitrate.

Organizational Affiliation

Unité de Chimie Organique et Médicinale, Université catholique de Louvain, Bâtiment Lavoisier, Place Louis Pasteur 1, B-1348 Louvain-la-Neuve, Belgium.

Macromolecule Content

Total Structure Weight: 59.41 kDa
Atom Count: 4,170
Modelled Residue Count: 510
Deposited Residue Count: 530
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, B	265	Bacillus licheniformis	Mutation(s): 0 EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808 Go to UniProtKB: P00808
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A33 Query on A33 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2-(carboxymethyl)-D-aspartic acid C₆ H₉ N O₆ ZJBWCVAEGNLETQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
A33	PDBBind: 3B3X	Ki: 2.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.288
R-Value Work: 0.220
R-Value Observed: 0.223
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.665	α = 90
b = 104.71	β = 93.96
c = 63.884	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description