6HMY

Cholera toxin classical B-pentamer in complex with fucosyl-GM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures reveal that Lewis-x and fucose bind to secondary cholera toxin binding site

Heim, J.B.Hodnik, V.Heggelund, J.E.Anderluh, G.Krengel, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholera enterotoxin B-subunit
A, B, C, D, E, F, G, H, I, J
103Vibrio choleraeMutation(s): 0 
Gene Names: ctxB
Find proteins for Q57193 (Vibrio cholerae)
Go to UniProtKB:  Q57193
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, J
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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A, B, C, D, E, F, G, H, I, J
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B, C, D, E, F, G, H, I, J
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BCN
Query on BCN

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A, B, D, E, I, J
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A, B, C, D, E, F, G, H, I, J
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
B, C, G, H
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NGA
Query on NGA

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Download CCD File 
A, B, C, D, E, F, G, H, I, J
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
A, B, C, D, E, F, G, H, I, J
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.626α = 90.00
b = 74.137β = 105.59
c = 111.245γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Cootmodel building
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway247730

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release