3ZNM

H5 Haemagglutinin in Complex with Sialyl-Lewis X

• PDB DOI: https://doi.org/10.2210/pdb3ZNM/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Vietnam/1194/2004(H5N1))
• Mutation(s): No 


• Deposited: 2013-02-15 Released: 2013-09-25 
• Deposition Author(s): Xiong, X., Tuzikov, A., Coombs, P., Martin, S.R., Walker, P.A., Gamblin, S.J., Bovin, N., Skehel, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.256 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Recognition of Sulphated and Fucosylated Receptor Sialosides by A/Vietnam/1194/2004 (H5N1) Influenza Virus.

Xiong, X., Tuzikov, A., Coombs, P., Martin, S., Walker, P.A., Gamblin, S.J., Bovin, N., Skehel, J.J.

(2013) Virus Res 178: 12

• PubMed: 24036174 
• DOI: https://doi.org/10.1016/j.virusres.2013.08.007
• Primary Citation of Related Structures:  
  3ZNK, 3ZNL, 3ZNM

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Organizational Affiliation: 

National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 173.31 kDa 
• Atom Count: 12,237 
• Modelled Residue Count: 1,452 
• Deposited Residue Count: 1,476 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ	A, C, E	326	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34  Go to UniProtKB:  Q6DQ34
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ	B, D, F	166	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34  Go to UniProtKB:  Q6DQ34
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	4		N/A
Glycosylation Resources
GlyTouCan:  G85849LM GlyCosmos:  G85849LM GlyGen:  G85849LM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	M [auth B], Q [auth D], U [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG	J [auth A], K [auth A], L [auth B], N [auth C], O [auth C], P [auth D], R [auth E], S [auth E], T [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.256 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.56	α = 90
b = 101.36	β = 111.29
c = 161.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Xiong, X., Tuzikov, A., Coombs, P., Martin, S.R., Walker, P.A., Gamblin, S.J., Bovin, N., Skehel, J.J.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Database references
• Version 1.2: 2015-01-21
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary