4XOG

CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH Optactin and DANA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 

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
660Streptococcus 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
OPX
Query on OPX

Download SDF File 
Download CCD File 
A
(1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid
C12 H23 N O5 S
RMLVAYWMDDDXFB-ZSBIGDGJSA-N
 Ligand Interaction
DMS
Query on DMS

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

Download SDF File 
Download CCD File 
A
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DANKi: 330000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.375α = 90.00
b = 82.498β = 90.00
c = 116.744γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-16 
  • Released Date: 2016-02-03 
  • Deposition Author(s): Brear, P.

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

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 2.0: 2017-08-30
    Type: Atomic model, Author supporting evidence, Derived calculations