5DQ9

Structure of S55-3 Fab in complex with Lipid A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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This is version 2.1 of the entry. See complete history. 


Literature

Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from from unrelated V-genes

Haji-Ghassemi, O., Muller-Loennies, S., Rodriguez, T., Brade, L., Kosma, P., Brade, H., Evans, S.V.

(2015) J Biol Chem 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S55-3 Fab (IgG2b) heavy chainA,
C,
E [auth H]		222Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MAb 44B1 light chainB,
D,
F [auth L]		218Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranoseG [auth E],
H [auth F],
I [auth G]		2N/A
Glycosylation Resources
GlyTouCan:  G84001BP
GlyCosmos:  G84001BP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 338.121α = 90
b = 52.865β = 100.95
c = 75.391γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary