6BKR
Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin in complex with 6'-SLN
- PDB DOI: https://doi.org/10.2210/pdb6BKR/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/Wyoming/3e/2003(H3)), Influenza A virus (A/Nymc X-149C6(Puerto Rico/8/1934-Wyoming/03/2003)(H3N2))
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2017-11-09 Released: 2018-02-28 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.76 Å
- R-Value Free: 0.183 
- R-Value Work: 0.159 
- R-Value Observed: 0.160 
This is version 3.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Hemagglutinin HA1 chain | 323 | Influenza A virus (A/Wyoming/3e/2003(H3)) | Mutation(s): 1  Gene Names: HA | ||
UniProt | |||||
Find proteins for A4GYF9 (Influenza A virus) Explore A4GYF9  Go to UniProtKB:  A4GYF9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A4GYF9 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Hemagglutinin HA2 chain | 174 | Influenza A virus (A/Nymc X-149C6(Puerto Rico/8/1934-Wyoming/03/2003)(H3N2)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for B4UPH9 (Influenza A virus) Explore B4UPH9  Go to UniProtKB:  B4UPH9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | B4UPH9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 | C, F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | D | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | H [auth A], I [auth A], J [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900046 Query on PRD_900046 | G | 6'-sialyl-N-acetyllactosamine | Oligosaccharide / Glycan component |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.76 Å
- R-Value Free: 0.183 
- R-Value Work: 0.159 
- R-Value Observed: 0.160 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 100.458 | α = 90 |
b = 100.458 | β = 90 |
c = 385.692 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data processing |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-28  Deposition Author(s): Wu, N.C., Wilson, I.A.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R56 AI117675 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R56 AI127371 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01 AI114730 |
Revision History (Full details and data files)
- Version 1.0: 2018-02-28
Type: Initial release - Version 2.0: 2018-03-14
Changes: Atomic model, Derived calculations, Structure summary - Version 2.1: 2018-04-11
Changes: Data collection, Database references - Version 2.2: 2019-12-11
Changes: Author supporting evidence, Data collection - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary