4XJU

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 4-acetamido-2-fluoro-3-hydroxy-6-[1,2-dihydroxyethyl]-7,8-dioxabicyclo[3.2.1]octane-1-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 2.0 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sialidase B
A
658Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 1 
Gene Names: nanB
EC: 3.2.1.18
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q54727
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
19D
Query on 19D

Download SDF File 
Download CCD File 
A
(1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid
C11 H16 F N O8
JCWSZUBTEOFKAD-DAXAGCIGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.414α = 90.00
b = 82.418β = 90.00
c = 116.697γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-09 
  • Released Date: 2016-01-13 
  • Deposition Author(s): Brear, P.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--
SULSAUnited Kingdom--

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 2.0: 2017-08-30
    Type: Atomic model, Author supporting evidence, Data collection, Derived calculations