2C5C

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2C5C/pdb

• Classification: TOXIN
• Organism(s): Phage h30
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-26 Released: 2006-11-27 
• Deposition Author(s): Dodd, R.B., Read, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.267 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Extensive Cross-Linking of the Shiga-Like Toxin 1 B Subunit by a Bivalent Ligand

Dodd, R.B., Read, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 88.12 kDa 
• Atom Count: 6,136 
• Modelled Residue Count: 690 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA-LIKE TOXIN 1 B SUBUNIT	A, B, C, D, E, F, G, H, I, J	69	Phage h30	Mutation(s): 0
UniProt
Find proteins for P69178 (Bacteriophage H30) Explore P69178  Go to UniProtKB:  P69178

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	CA [auth c], DA [auth d], K, L, M, N, O, Q, V, Y	3		N/A
Glycosylation Resources
GlyTouCan:  G79094AA GlyCosmos:  G79094AA GlyGen:  G79094AA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose	P, R, U, W, X, Z	2		N/A
Glycosylation Resources
GlyTouCan:  G54046EC GlyCosmos:  G54046EC GlyGen:  G54046EC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	S, T	3		N/A
Glycosylation Resources
GlyTouCan:  G00059MO GlyCosmos:  G00059MO GlyGen:  G00059MO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose	AA [auth a], BA [auth b]	3		N/A
Glycosylation Resources
GlyTouCan:  G80589WZ GlyCosmos:  G80589WZ GlyGen:  G80589WZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S10	EA [auth A], GA [auth C], HA [auth D], IA [auth E], JA [auth F], KA [auth I], MA [auth J], NA [auth J]	DIETHYL PROPANE-1,3-DIYLBISCARBAMATE C9 H18 N2 O4 BWWHOVJFNMPUKF-UHFFFAOYSA-N
GLA	FA [auth C]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
SO4	LA [auth I]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.267 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.313	α = 90
b = 114.313	β = 90
c = 406.936	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-27 
Deposition Author(s): Dodd, R.B., Read, R.J.

Revision History  

• Version 1.0: 2006-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2018-12-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2020-07-01
  Changes: Data collection, Other
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary