RCSB PDB - 9C0V: Crystal structure of chimeric hemagglutinin cH5/1 in complex with broad protective antibody 3E1

 9C0V

Crystal structure of chimeric hemagglutinin cH5/1 in complex with broad protective antibody 3E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.0 of the entry. See complete history


Literature

Crystal structure of chimeric hemagglutinin cH5/1 in complex with broad protective antibody 3E1

Nguyen, T.K.Y.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, B
541Influenza A virusMutation(s): 0 
Gene Names: HA
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 3E1 Fab heavy chainC [auth H]224Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 3E1 Fab light chainD [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth S],
F [auth C]
3N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.491α = 90
b = 241.491β = 90
c = 241.491γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93109C00051

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release