4GZX

N2 neuraminidase D151G mutant of A/Tanzania/205/2010 H3N2 in complex with human sialic acid receptor

• PDB DOI: https://doi.org/10.2210/pdb4GZX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): H3N2 subtype
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-09-06 Released: 2012-10-17 
• Deposition Author(s): Zhu, X., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 181.72 kDa 
• Atom Count: 13,064 
• Modelled Residue Count: 1,552 
• Deposited Residue Count: 1,572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
neuraminidase	A, B, C, D	393	H3N2 subtype	Mutation(s): 0
UniProt
Find proteins for K7N5N3 (H3N2 subtype) Explore K7N5N3  Go to UniProtKB:  K7N5N3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	E, G	2		N/A
Glycosylation Resources
GlyTouCan:  G63069TR GlyCosmos:  G63069TR GlyGen:  G63069TR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	F, H, I, K	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G95595RA GlyCosmos:  G95595RA GlyGen:  G95595RA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	V [auth C], Z [auth D]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	AA [auth D], BA [auth D], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	CA [auth D], P [auth A], Q [auth A], U [auth B], Y [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SIA	PDBBind:  4GZX	Kd: 6.45e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.587	α = 90
b = 110.176	β = 97.45
c = 110.043	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary