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: 3.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A, B, C
327Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)Mutation(s): 0 
Gene Names: HA
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6))
Go to UniProtKB:  A3KF09
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
D, E, F
176Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)Mutation(s): 0 
Gene Names: HA
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6))
Go to UniProtKB:  A3KF09
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
a group 2 HA binding antibody AF4H1K1 Fab heavy chain
I, K
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
a group 2 HA binding antibody AF4H1K1 Fab light chain
J, L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 114.175α = 90.00
b = 140.940β = 95.31
c = 138.100γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release