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
Currently 6MYM does not have a validation slider image.
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
Currently 6MYM does not have a validation slider image.
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
