9E55 | pdb_00009e55

Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with cyclic peptide iHA-100

• PDB DOI: https://doi.org/10.2210/pdb9E55/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus, Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-10-27 Released: 2025-10-08 
• Deposition Author(s): Nguyen, T.K.Y., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.312 (Depositor), 0.331 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.311 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with cyclic peptide iHA-100

Nguyen, T.K.Y., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A3B3C1D1E1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.99 kDa 
• Atom Count: 4,144 
• Modeled Residue Count: 515 
• Deposited Residue Count: 515 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 subunit	A	323	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A2P1MB68 (Influenza A virus) Explore A0A2P1MB68  Go to UniProtKB:  A0A2P1MB68

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 subunit	B	176	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A2P1MB68 (Influenza A virus) Explore A0A2P1MB68  Go to UniProtKB:  A0A2P1MB68

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IHA-100 peptide	C [auth P]	16	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth S]	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.312 (Depositor), 0.331 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.311 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.729	α = 90
b = 100.729	β = 90
c = 328.684	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Nguyen, T.K.Y., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release