5VMG
Influenza hemagglutinin H1 mutant DH1E in complex with 6'SLN
- PDB DOI: https://doi.org/10.2210/pdb5VMG/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/New_York/1/18(H1N1)), Influenza A virus (A/Brevig Mission/1/1918(H1N1))
- Expression System: unidentified baculovirus
- Mutation(s): Yes 
- Deposited: 2017-04-27 Released: 2017-11-08 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.225 
- R-Value Work: 0.191 
- R-Value Observed: 0.193 
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/New_York/1/18(H1N1)) | Mutation(s): 3  Gene Names: HA | ||
UniProt | |||||
Find proteins for Q9WFX4 (Influenza A virus) Explore Q9WFX4  Go to UniProtKB:  Q9WFX4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9WFX4 | ||||
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 | 191 | Influenza A virus (A/Brevig Mission/1/1918(H1N1)) | Mutation(s): 0  Gene Names: HA | ||
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 | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | H, I | 2 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G63069TR GlyCosmos:  G63069TR GlyGen:  G63069TR |
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 C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900046 Query on PRD_900046 | K | 6'-sialyl-N-acetyllactosamine | Oligosaccharide / Glycan component |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.225 
- R-Value Work: 0.191 
- R-Value Observed: 0.193 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 95.38 | α = 90 |
b = 81.37 | β = 95.45 |
c = 120.96 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-11-08  Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01-AI067839 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01-GM116280 |
Revision History (Full details and data files)
- Version 1.0: 2017-11-08
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2022-03-23
Changes: Author supporting evidence, Database references, Derived calculations, Structure summary - Version 2.2: 2023-10-04
Changes: Data collection, Refinement description