1QFU

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY

PDB DOI: https://doi.org/10.2210/pdb1QFU/pdb

Classification: Viral protein/Immune system
Organism(s): Influenza A virus (A/X-31(H3N2)), Mus musculus
Mutation(s): No

Deposited: 1999-04-14 Released: 1999-04-16
Deposition Author(s): Fleury, D., Gigant, B., Bizebard, T., Daniels, R.S., Skehel, J.J., Knossow, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 106.36 kDa
Atom Count: 7,439
Modelled Residue Count: 932
Deposited Residue Count: 943
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMAGGLUTININ (HA1 CHAIN))	A	328	Influenza A virus (A/X-31(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2)) Explore P03438 Go to UniProtKB: P03438
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03438
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMAGGLUTININ (HA2 CHAIN))	B	175	Influenza A virus (A/X-31(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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03437
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))	C [auth L]	217	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3 Go to UniProtKB: A2NHM3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2NHM3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))	D [auth H]	223	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01869 (Mus musculus) Explore P01869 Go to UniProtKB: P01869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01869
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation	Interactions Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G07375KG GlyCosmos: G07375KG GlyGen: G07375KG

Entity ID: 6
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	F [auth D]	3		N-Glycosylation	Interactions Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B]	G [auth A], H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.198
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138	α = 90
b = 138	β = 90
c = 135	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-04-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-04-16
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-03-08
Changes: Derived calculations
Version 1.4: 2017-10-04
Changes: Refinement description
Version 1.5: 2019-11-27
Changes: Database references, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary