4XQU
Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza virus in complex with 3'-SLN
- PDB DOI: https://doi.org/10.2210/pdb4XQU/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/Jiangxi/IPB13/2013(H10N8))
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2015-01-20 Released: 2015-04-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.261 
- R-Value Work: 0.217 
- R-Value Observed: 0.219 
This is version 2.2 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 | 326 | Influenza A virus (A/Jiangxi/IPB13/2013(H10N8)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1  Go to UniProtKB:  A0A059T4A1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A059T4A1 | ||||
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 | 181 | Influenza A virus (A/Jiangxi/IPB13/2013(H10N8)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1  Go to UniProtKB:  A0A059T4A1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A059T4A1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G, I | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | L [auth A], M [auth C], N [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, I | 3'-sialyl-N-acetyllactosamine | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.261 
- R-Value Work: 0.217 
- R-Value Observed: 0.219 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 64.874 | α = 90 |
b = 245.853 | β = 112.46 |
c = 70.995 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHENIX | model building |
PHENIX | phasing |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2015-04-01  Deposition Author(s): Tzarum, N., Zhang, H., Zhu, X., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2015-04-01
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary - Version 2.1: 2021-09-01
Changes: Database references, Derived calculations, Structure summary - Version 2.2: 2023-09-27
Changes: Data collection, Refinement description