6P3S

Crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

• PDB DOI: https://doi.org/10.2210/pdb6P3S/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-05-24 Released: 2020-05-27 
• Deposition Author(s): Dong, J., Crowe, J.E.
• 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: 4.00 Å
• R-Value Free: 0.326 
• R-Value Work: 0.281 
• R-Value Observed: 0.283 

Literature

crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

Dong, J., Crowe, J.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 596.23 kDa 
• Atom Count: 32,097 
• Modelled Residue Count: 4,991 
• Deposited Residue Count: 5,312 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.28 heavy chain	A, C, F, I, M, P, S, V	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.28 light chain	B, D, G, J, N, Q, T, W	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	E, H, K, L, O, R, U, X	219	Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q1KHK2 (Influenza A virus) Explore Q1KHK2  Go to UniProtKB:  Q1KHK2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G59070FK GlyCosmos:  G59070FK GlyGen:  G59070FK

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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	Z	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G13564MD GlyCosmos:  G13564MD GlyGen:  G13564MD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	6		N/A
Glycosylation Resources
GlyTouCan:  G20631NH GlyCosmos:  G20631NH GlyGen:  G20631NH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G87077ZT GlyCosmos:  G87077ZT GlyGen:  G87077ZT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose	CA [auth c]	5		N/A
Glycosylation Resources
GlyTouCan:  G19798XY GlyCosmos:  G19798XY GlyGen:  G19798XY

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d]	7		N/A
Glycosylation Resources
GlyTouCan:  G77499AE GlyCosmos:  G77499AE GlyGen:  G77499AE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose	EA [auth e]	5		N/A
Glycosylation Resources
GlyTouCan:  G89628EO GlyCosmos:  G89628EO GlyGen:  G89628EO

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-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	FA [auth f]	7		N/A
Glycosylation Resources
GlyTouCan:  G84134OD GlyCosmos:  G84134OD GlyGen:  G84134OD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	GA [auth L], HA [auth O], IA [auth R], JA [auth U], KA [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.326 
• R-Value Work: 0.281 
• R-Value Observed: 0.283 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.48	α = 90
b = 187.225	β = 90
c = 342.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Currently 6P3S does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Dong, J., Crowe, J.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5U19AI117905-05

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary