5Y2M

Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins

Xiao, H.Qi, J.Gao, F.G.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininA,
C [auth B],
E [auth C]
327Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6))
Explore A3KF09 
Go to UniProtKB:  A3KF09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3KF09
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininB [auth D],
D [auth E],
F
176Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6))
Explore A3KF09 
Go to UniProtKB:  A3KF09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3KF09
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
a group 2 HA binding antibody AF4H1K1 Fab heavy chainG [auth I],
I [auth K]
233Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
a group 2 HA binding antibody AF4H1K1 Fab light chainH [auth J],
J [auth L]
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.175α = 90
b = 140.94β = 95.31
c = 138.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary