6E3H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 virusMutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2
B
175Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody S9-3-37 light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
antibody S9-3-37 heavy chain
H
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 157.269α = 90.00
b = 157.269β = 90.00
c = 345.167γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 DiseasesUnited StatesR56 AI127371

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2018-10-10
    Type: Data collection, Database references, Source and taxonomy, Structure summary