4CYW
Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with human receptor analog 6-SLN
- PDB DOI: https://doi.org/10.2210/pdb4CYW/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/mallard/Sweden/51/2002(H10N2))
- Mutation(s): No 
- Deposited: 2014-04-15 Released: 2014-06-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.254 
- R-Value Work: 0.208 
- R-Value Observed: 0.211 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
HEMAGGLUTININ | 324 | Influenza A virus (A/mallard/Sweden/51/2002(H10N2)) | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for E0YNJ7 (Influenza A virus) Explore E0YNJ7  Go to UniProtKB:  E0YNJ7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | E0YNJ7 | ||||
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 | 173 | Influenza A virus (A/mallard/Sweden/51/2002(H10N2)) | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for E0YNJ7 (Influenza A virus) Explore E0YNJ7  Go to UniProtKB:  E0YNJ7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | E0YNJ7 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G, I, K | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G73578JC GlyCosmos:  G73578JC GlyGen:  G73578JC |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42769XG GlyCosmos:  G42769XG GlyGen:  G42769XG |
Entity ID: 6 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | L | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | M [auth A] N [auth A] O [auth C] P [auth C] Q [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_900046 Query on PRD_900046 | G, I, K | 6'-sialyl-N-acetyllactosamine | Oligosaccharide / Glycan component |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.254 
- R-Value Work: 0.208 
- R-Value Observed: 0.211 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 68.973 | α = 90 |
b = 215.446 | β = 104.91 |
c = 79.363 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2014-06-11  Deposition Author(s): Vachieri, S.G., Xiong, X., Collins, P.J., Walker, P.A., Martin, S.R., Haire, L.F., McCauley, J.W., Gamblin, S.J., Skehel, J.J.
Revision History (Full details and data files)
- Version 1.0: 2014-06-11
Type: Initial release - Version 1.1: 2014-06-25
Changes: Atomic model, Derived calculations, Other - Version 1.2: 2014-07-30
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary