3ZNK

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HAEMAGGLUTININ
A, C, E
326Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q6DQ34 (Influenza A virus)
Explore Q6DQ34 
Go to UniProtKB:  Q6DQ34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ34
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HAEMAGGLUTININ
B, D, F
166Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q6J8F6 (Influenza A virus (strain A/Hong Kong/212/2003 H5N1 genotype Z+))
Explore Q6J8F6 
Go to UniProtKB:  Q6J8F6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6J8F6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose
G, H, I
3N/A
Glycosylation Resources
GlyTouCan:  G54421JX
GlyCosmos:  G54421JX
GlyGen:  G54421JX
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
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
Query on NAG
Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth B]
N [auth C]
O [auth C]
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: 2.71 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.34α = 90
b = 101.23β = 111.31
c = 160.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • 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