1Z4X

Parainfluenza Virus 5 (SV5) Hemagglutinin-Neuraminidase (HN) with ligand Sialyllactose (soaked with Sialyllactose, pH8.0)

• PDB DOI: https://doi.org/10.2210/pdb1Z4X/pdb

• Classification: HYDROLASE
• Organism(s): Mammalian orthorubulavirus 5
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2005-03-16 Released: 2005-05-24 
• Deposition Author(s): Yuan, P., Thompson, T.B., Wurzburg, B.A., Paterson, R.G., Lamb, R.A., Jardetzky, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.204 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 60.25 kDa 
• Atom Count: 3,847 
• Modelled Residue Count: 448 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase	A	532	Mammalian orthorubulavirus 5	Mutation(s): 0  Gene Names: HN EC: 3.2.1.18
UniProt
Find proteins for P04850 (Parainfluenza virus 5 (strain W3)) Explore P04850  Go to UniProtKB:  P04850

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	D	3		N/A
Glycosylation Resources
GlyTouCan:  G92323ZH GlyCosmos:  G92323ZH GlyGen:  G92323ZH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900025	D	3'-sialyl-alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.204 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.112	α = 90
b = 137.112	β = 90
c = 184.368	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Yuan, P., Thompson, T.B., Wurzburg, B.A., Paterson, R.G., Lamb, R.A., Jardetzky, T.S.

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary