4MSS

Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-acetamido-4,5,6-trihydroxyazepane

PDB DOI: https://doi.org/10.2210/pdb4MSS/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-18 Released: 2013-10-30
Deposition Author(s): Vadlamani, G., Mark, B.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190
R-Value Work: 0.135

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to beta-lactams.

Mondon, M., Hur, S., Vadlamani, G., Rodrigues, P., Tsybina, P., Oliver, A., Mark, B.L., Vocadlo, D.J., Bleriot, Y.

(2013) Chem Commun (Camb) 49: 10983-10985

PubMed: 24136176 Search on PubMed
DOI: https://doi.org/10.1039/c3cc46646a
Primary Citation of Related Structures:
4MSS

PubMed Abstract:
AmpC β-lactamase confers resistance to β-lactam antibiotics in many Gram negative bacteria. Inducible expression of AmpC requires an N-acetylglucosaminidase termed NagZ. Here we describe the synthesis and characterization of hydroxyazepane inhibitors of NagZ. We find that these inhibitors enhance the susceptibility of clinically relevant Pseudomonas aeruginosa to β-lactams.

Organizational Affiliation

Université de Poitiers, IC2MP, UMR CNRS 7285, Équipe "Synthése Organique" Groupe Glycochimie, 4 rue Michel Brunet, 86022 Poitiers Cedex, France. yves.bleriot@univ-poitiers.fr.

Macromolecule Content

Total Structure Weight: 76.92 kDa
Atom Count: 5,972
Modelled Residue Count: 679
Deposited Residue Count: 700
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-hexosaminidase 1	A, B	350	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL1010, BCAL2860, BceJ2315_10000, BceJ2315_27960, nagZ, nagZ1, nagZ2 EC: 3.2.1.52
UniProt
Find proteins for B4EA43 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EA43 Go to UniProtKB: B4EA43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EA43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2CZ Query on 2CZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide C₈ H₁₆ N₂ O₄ RGHXJBVAPJFIEQ-RULNZFCNSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B]	D [auth A], F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
2CZ	Binding MOAD: 4MSS	Ki: 3600 (nM) from 1 assay(s)
2CZ	PDBBind: 4MSS	Ki: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190
R-Value Work: 0.135
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.76	α = 90
b = 87.58	β = 92.1
c = 67.21	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Vadlamani, G.

Mark, B.L.

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2013-11-13
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description