4GZT

N2 neuraminidase D151G mutant of A/Tanzania/205/2010 H3N2 in complex with oseltamivir carboxylate

• PDB DOI: https://doi.org/10.2210/pdb4GZT/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: 2.19 Å
• R-Value Free: 0.260 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

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: 181.42 kDa 
• Atom Count: 13,132 
• 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
beta-D-mannopyranose-(1-3)-[beta-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	E, G, H, J	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G89225LT GlyCosmos:  G89225LT GlyGen:  G89225LT

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	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA GlyCosmos:  G63564LA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G39	L [auth A], Q [auth B], V [auth C], Y [auth D]	(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid C14 H24 N2 O4 NENPYTRHICXVCS-YNEHKIRRSA-N
NAG	AA [auth D], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], W [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	BA [auth D], O [auth A], P [auth A], U [auth B], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G39	Binding MOAD:  4GZT	Ki: 17 (nM) from 1 assay(s)
	PDBBind:  4GZT	Ki: 17 (nM) from 1 assay(s)
	BindingDB:  4GZT	IC50: min: 0.11, max: 170 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.260 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.244	α = 90
b = 110.194	β = 98.27
c = 109.847	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: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary