4XJA

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb4XJA/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-01-08 Released: 2016-01-20
Deposition Author(s): Brear, P.
Funding Organization(s): Biotechnology and Biological Sciences Research Council, SULSA

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.201
R-Value Work: 0.167
R-Value Observed: 0.169

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

`The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB

Rogers, G.W., Brear, P., Yang, L., Chen, A.S., Mitchell, J.B.O., Taylor, G.L., Westwood, N.J.

To be published.

Macromolecule Content

Total Structure Weight: 74.39 kDa
Atom Count: 5,840
Modelled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase B	A	658	Streptococcus pneumoniae TIGR4	Mutation(s): 1 Gene Names: nanB, SP_1687 EC: 3.2.1.18
UniProt
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54727 Go to UniProtKB: Q54727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q54727
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFJ Query on SFJ Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid C₁₁ H₁₇ F₂ N O₈ HMALKZAXODOYOP-DAXAGCIGSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
OPX Query on OPX Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid C₁₂ H₂₃ N O₅ S RMLVAYWMDDDXFB-ZSBIGDGJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.201
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.586	α = 90
b = 82.556	β = 90
c = 116.654	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Brear, P.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--
SULSA	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-01-20
Type: Initial release
Version 2.0: 2017-08-30
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Derived calculations, Structure summary
Version 3.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary