4KDN
Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with avian receptor analog LSTa
- PDB DOI: https://doi.org/10.2210/pdb4KDN/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2013-04-25 Released: 2013-07-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.48 Å
- R-Value Free: 0.259 
- R-Value Work: 0.223 
- R-Value Observed: 0.225 
This is version 2.0 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 | 322 | Influenza A virus (A/Viet Nam/1203/2004(H5N1)) | Mutation(s): 4  Gene Names: HA | ||
UniProt | |||||
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33  Go to UniProtKB:  Q6DQ33 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6DQ33 | ||||
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 | 175 | Influenza A virus (A/Viet Nam/1203/2004(H5N1)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33  Go to UniProtKB:  Q6DQ33 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6DQ33 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SIA Query on SIA | K [auth A], M [auth C] | N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N | |||
NAG Query on NAG | J [auth A], L [auth C], N [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.48 Å
- R-Value Free: 0.259 
- R-Value Work: 0.223 
- R-Value Observed: 0.225 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 66.68 | α = 90 |
b = 245.156 | β = 113.75 |
c = 68.557 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
Revision History (Full details and data files)
- Version 1.0: 2013-07-24
Type: Initial release - Version 1.1: 2013-09-04
Changes: Database references - Version 1.2: 2014-10-29
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary