2AEP

An epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex.

• PDB DOI: https://doi.org/10.2210/pdb2AEP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/Memphis/31/98(H3N2)), Mus musculus
• Mutation(s): No 


• Deposited: 2005-07-23 Released: 2005-12-20 
• Deposition Author(s): Venkatramani, L., Bochkareva, E., Lee, J.T., Gulati, U., Laver, W.G., Bochkarev, A., Air, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Cyclic - C4  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A8B4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.74 kDa 
• Atom Count: 5,812 
• Modelled Residue Count: 660 
• Deposited Residue Count: 826 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
neuraminidase	A	395	Influenza A virus (A/Memphis/31/98(H3N2))	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for Q9DL16 (Influenza A virus) Explore Q9DL16  Go to UniProtKB:  Q9DL16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB heavy chain	B [auth H]	217	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P84751 (Mus musculus) Explore P84751  Go to UniProtKB:  P84751

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB light chain	C [auth L]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P84750 (Mus musculus) Explore P84750  Go to UniProtKB:  P84750

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G23799GS GlyCosmos:  G23799GS GlyGen:  G23799GS

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	M [auth L]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
GLC	E [auth A], L [auth H]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4	K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.057	α = 90
b = 155.057	β = 90
c = 102.645	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Venkatramani, L., Bochkareva, E., Lee, J.T., Gulati, U., Laver, W.G., Bochkarev, A., Air, G.M.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary