3VUN | pdb_00003vun

Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group.

PDB DOI: https://doi.org/10.2210/pdb3VUN/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Aichi/2/1968(H3N2))
Mutation(s): No

Deposited: 2012-07-02 Released: 2012-08-01
Deposition Author(s): Yasutake, Y., Suzuki, T., Kawaguchi, A., Nobusawa, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.275 (Depositor), 0.271 (DCC)
R-Value Work:
0.216 (Depositor), 0.213 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group

Yasutake, Y., Suzuki, T., Kawaguchi, A., Nobusawa, E.

To be published.

Macromolecule Content

Total Structure Weight: 179.03 kDa
Atom Count: 12,255
Modeled Residue Count: 1,476
Deposited Residue Count: 1,512
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	329	Influenza A virus (A/Aichi/2/1968(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437 Go to UniProtKB: P03437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03437
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	175	Influenza A virus (A/Aichi/2/1968(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437 Go to UniProtKB: P03437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03437
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, M	9		N-Glycosylation	Interactions Focus chain G Focus chain J Focus chain M Interactions & Density Focus chain G Focus chain J Focus chain M
Glycosylation Resources
GlyTouCan: G27919IH GlyCosmos: G27919IH GlyGen: G27919IH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, N	2		N-Glycosylation	Interactions Focus chain H Focus chain K Focus chain N Interactions & Density Focus chain H Focus chain K Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	I, L, O	4		N-Glycosylation	Interactions Focus chain I Focus chain L Focus chain O Interactions & Density Focus chain I Focus chain L Focus chain O
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth F] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F]	P [auth A] Q [auth B] R [auth C] S [auth D] T [auth E] P [auth A], Q [auth B], R [auth C], S [auth D], T [auth E], U [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Interactions & Density Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.275 (Depositor), 0.271 (DCC)
R-Value Work: 0.216 (Depositor), 0.213 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.016	α = 90
b = 98.13	β = 113.11
c = 144.776	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary