6E3H

Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The D3-9 gene segment encodes for recurring and adaptable binding motifs in broadly neutralizing antibodies to influenza virus

Wu, N.C.Yamayoshi, S.Ito, M.Uraki, R.Kawaoka, Y.Wilson, I.A.

(2018) Cell Host Microbe 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1
A
324Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2
B
175Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody S9-3-37 light chain
L
219Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
antibody S9-3-37 heavy chain
H
233Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.269α = 90
b = 157.269β = 90
c = 345.167γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-14 
  • Released Date: 2018-09-26 
  • Deposition Author(s): Wu, N.C., Wilson, I.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI127371

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Data collection, Structure summary