2C5C

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


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 

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA-LIKE TOXIN 1 B SUBUNIT
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
69Phage h30Mutation(s): 0 
Gene Names: stxB
UniProt
Find proteins for P69178 (Bacteriophage H30)
Explore P69178 
Go to UniProtKB:  P69178
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69178
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
CA [auth c],
DA [auth d],
K,
L,
M,
CA [auth c],
DA [auth d],
K,
L,
M,
N,
O,
Q,
V,
Y
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G79094AA
GlyCosmos:  G79094AA
GlyGen:  G79094AA
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose
P, R, U, W, X, Z
P, R, U, W, X, Z
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G54046EC
GlyCosmos:  G54046EC
GlyGen:  G54046EC
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseS, T 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G00059MO
GlyCosmos:  G00059MO
GlyGen:  G00059MO
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranoseAA [auth a],
BA [auth b]
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80589WZ
GlyCosmos:  G80589WZ
GlyGen:  G80589WZ
Small Molecules
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 = 114.313α = 90
b = 114.313β = 90
c = 406.936γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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