4PY8
Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin
- PDB DOI: https://doi.org/10.2210/pdb4PY8/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Influenza A virus (A/South Carolina/1/1918(H1N1)), Homo sapiens
- Expression System: Trichoplusia ni, Escherichia coli
- Mutation(s): No 
- Deposited: 2014-03-26 Released: 2014-05-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.242 
- R-Value Work: 0.193 
- R-Value Observed: 0.196 
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 HA1 chain | 331 | Influenza A virus (A/South Carolina/1/1918(H1N1)) | Mutation(s): 0  Gene Names: HA, hemagglutinin | ||
UniProt | |||||
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9WFX3 | ||||
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 | 179 | Influenza A virus (A/South Carolina/1/1918(H1N1)) | Mutation(s): 0  Gene Names: HA, hemagglutinin | ||
UniProt | |||||
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9WFX3 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
antibody 3.1 heavy chain | C [auth I] | 219 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
antibody 3.1 light chain | D [auth J] | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
MLI Query on MLI | H [auth I], I [auth J] | MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.242 
- R-Value Work: 0.193 
- R-Value Observed: 0.196 
- Space Group: H 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 135.06 | α = 90 |
b = 135.06 | β = 90 |
c = 230.201 | γ = 120 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-05-21  Deposition Author(s): Dreyfus, C.
Revision History (Full details and data files)
- Version 1.0: 2014-05-21
Type: Initial release - Version 1.1: 2014-06-04
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary