6FYW
Structure of B/Brisbane/60/2008 Influenza Hemagglutinin in complex with SD83
- PDB DOI: https://doi.org/10.2210/pdb6FYW/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza B virus (B/Brisbane/60/2008), Lama glama
- Expression System: Spodoptera frugiperda, Homo sapiens
- Mutation(s): No
- Deposited: 2018-03-12 Released: 2018-11-07
- Funding Organization(s): National Institutes of Health
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.218
- R-Value Work: 0.193
- R-Value Observed: 0.193
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 | 347 | Influenza B virus (B/Brisbane/60/2008) | Mutation(s): 0 Gene Names: HA |  | |
UniProt | |||||
Find proteins for C0LT35 (Influenza B virus) Explore C0LT35 Go to UniProtKB: C0LT35 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C0LT35 | ||||
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 | 179 | Influenza B virus (B/Brisbane/60/2008) | Mutation(s): 0 Gene Names: HA |  | |
UniProt | |||||
Find proteins for C0LT38 (Influenza B virus) Explore C0LT38 Go to UniProtKB: C0LT38 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C0LT38 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Single domain antibody SD83 | 129 | Lama glama | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| 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 | D | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 | E | 7 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F, G | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-2)-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 | H | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | I [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| GOL Query on GOL | J [auth A], K [auth A], L [auth A], M [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.218
- R-Value Work: 0.193
- R-Value Observed: 0.193
- Space Group: I 21 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 189.04 | α = 90 |
| b = 189.04 | β = 90 |
| c = 189.04 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-11-07 Deposition Author(s): Laursen, N.S., Wilson, I.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health | United States | R56 AI117675 |
| National Institutes of Health | United States | R56 AI127371 |
Revision History (Full details and data files)
- Version 1.0: 2018-11-07
Type: Initial release - Version 1.1: 2018-11-14
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
