6MYM
Crystal structure of hemagglutinin from influenza virus A/Phillipines/2/1982 (H3N2)
- PDB DOI: https://doi.org/10.2210/pdb6MYM/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/Philippines/2/1982(H3N2))
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2018-11-01 Released: 2019-05-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.254 
- R-Value Work: 0.227 
- R-Value Observed: 0.228 
wwPDB Validation   3D Report Full Report
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This is version 2.1 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 | 497 | Influenza A virus (A/Philippines/2/1982(H3N2)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for D8KS88 (Influenza A virus (strain A/Philippines/2/1982 H3N2)) Explore D8KS88  Go to UniProtKB:  D8KS88 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | D8KS88 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, E, H, K, L D, E, H, K, L, N, P | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
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 | F, G, I, J, M F, G, I, J, M, O, Q | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG (Subject of Investigation/LOI) Query on NAG | R [auth A] S [auth B] T [auth B] U [auth B] V [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.254 
- R-Value Work: 0.227 
- R-Value Observed: 0.228 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 195.78 | α = 90 |
b = 187.58 | β = 109.82 |
c = 107.73 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Structure Validation
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Entry History 
Deposition Data
- Released Date: 2019-05-15  Deposition Author(s): Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2019-05-15
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: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary