4FNK

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb4FNK/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2012-06-19 Released: 2012-09-19
Deposition Author(s): Ekiert, D.C., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.189
R-Value Work: 0.162
R-Value Observed: 0.163

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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 173.75 kDa
Atom Count: 14,165
Modelled Residue Count: 1,467
Deposited Residue Count: 1,491
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	323	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91MA7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	174	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91MA7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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	H, I, J, L, M H, I, J, L, M, O	2		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain O Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	3		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	N	5		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	CA [auth F] P [auth A] Q [auth A] R [auth A] T [auth B] CA [auth F], P [auth A], Q [auth A], R [auth A], T [auth B], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain Y [auth E] Focus chain Z [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D]	AA [auth E] DA [auth F] S [auth A] U [auth B] W [auth D] AA [auth E], DA [auth F], S [auth A], U [auth B], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain V [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain V [auth C]	BA [auth E], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain V [auth C] Interactions & Density Focus chain BA [auth E] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.189
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.149	α = 90
b = 151.458	β = 90
c = 347.751	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Ekiert, D.C.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2012-10-03
Changes: Database references
Version 1.2: 2012-10-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4FNK

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)