4KPS

Structure and receptor binding specificity of the hemagglutinin H13 from avian influenza A virus H13N6

• PDB DOI: https://doi.org/10.2210/pdb4KPS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/gull/Maryland/704/1977(H13N6))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-05-14 Released: 2013-07-03 
• Deposition Author(s): Lu, X., Qi, J., Shi, Y., Gao, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 166.52 kDa 
• Atom Count: 11,796 
• Modelled Residue Count: 1,467 
• Deposited Residue Count: 1,467 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E	324	Influenza A virus (A/gull/Maryland/704/1977(H13N6))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P13103 (Influenza A virus (strain A/Gull/Maryland/704/1977 H13N6)) Explore P13103  Go to UniProtKB:  P13103

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F	165	Influenza A virus (A/gull/Maryland/704/1977(H13N6))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P13103 (Influenza A virus (strain A/Gull/Maryland/704/1977 H13N6)) Explore P13103  Go to UniProtKB:  P13103

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	G	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	H	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.638	α = 85.6
b = 76.804	β = 82.67
c = 76.38	γ = 87.52

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Lu, X., Qi, J., Shi, Y., Gao, G.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary