6TYO

Salmonella Typhi PltB Homopentamer with Neu-5NAc-4OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication

Nguyen, T.Lee, S.Yang, Y.A.Sim, J.H.Kei, T.G.Barnard, K.N.Yu, H.Millano, S.K.Chen, X.Parrish, C.Song, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pertussis-like toxin subunit
A, B, C, D, E
114Salmonella typhiMutation(s): 0 
Find proteins for Q8Z6A3 (Salmonella typhi)
Go to UniProtKB:  Q8Z6A3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PKM
Query on PKM

Download SDF File 
Download CCD File 
A, C, D, E
4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
C13 H21 N O10
LVBIMVQYUKOENY-CYBLFPARSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, C, D, E
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.580α = 90.00
b = 98.208β = 90.00
c = 104.602γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI137345
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI139625
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI141514
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03 AI135767

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release