2C4A | pdb_00002c4a

Structure of Neuraminidase Subtype N9 Complexed with 30 MM Sialic Acid (NANA, NEU5AC), Crystal Soaked for 3 Hours at 291 K.

• PDB DOI: https://doi.org/10.2210/pdb2C4A/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus
• Expression System: Gallus gallus
• Mutation(s): No 


• Deposited: 2005-10-17 Released: 2007-03-27 
• Deposition Author(s): Rudino-Pinera, E., Tunnah, P., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Influenza Type a Virus Neuraminidase of the N6 Subtype at 1.85 A Resolution

Rudino-Pinera, E., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 46.59 kDa 
• Atom Count: 3,516 
• Modeled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAMINIDASE SUBTYPE N9	A	388	Influenza A virus	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)) Explore P03472  Go to UniProtKB:  P03472
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	B	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB GlyCosmos:  G68668TB GlyGen:  G68668TB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	D [auth A], E [auth A]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.336	α = 90
b = 181.336	β = 90
c = 181.336	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Rudino-Pinera, E., Tunnah, P., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary