5T0D
Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza virus in complex with 3'-SLN
- PDB DOI: https://doi.org/10.2210/pdb5T0D/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): H6N1 subtype
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2016-08-15 Released: 2017-06-14 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.245 
- R-Value Work: 0.206 
- R-Value Observed: 0.208 
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 | 333 | H6N1 subtype | Mutation(s): 1  Gene Names: HA | ||
UniProt | |||||
Find proteins for A0A0J9X268 (H6N1 subtype) Explore A0A0J9X268  Go to UniProtKB:  A0A0J9X268 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0J9X268 | ||||
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 | 180 | H6N1 subtype | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for A0A0J9X267 (H6N1 subtype) Explore A0A0J9X267  Go to UniProtKB:  A0A0J9X267 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0J9X267 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900067 Query on PRD_900067 | G | 3'-sialyl-N-acetyllactosamine | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.245 
- R-Value Work: 0.206 
- R-Value Observed: 0.208 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 185.056 | α = 90 |
b = 98.733 | β = 126.76 |
c = 132.787 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-06-14  Deposition Author(s): Wilson, I.A., Tzarum, N., Zhu, X.
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 | AI114730 |
Revision History (Full details and data files)
- Version 1.0: 2017-06-14
Type: Initial release - Version 1.1: 2017-07-26
Changes: Author supporting evidence, Database references - Version 1.2: 2017-09-13
Changes: Database references - Version 1.3: 2017-11-22
Changes: Refinement description - Version 1.4: 2019-12-11
Changes: Author supporting evidence, Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary